Stream 1.1 Error

[bellenger-l]

Hello,

I'm having trouble upgrading the version of STREAM. While before I had no errors, now none of my scripts work.
I work with conda environments and here is the version of the main packages:

With STREAM 1.0 (where everything is fine) :

print(stream.__version__)
print(scanpy.__version__)
print(pandas.__version__)
print(matplotlib.__version__)
print(numpy.__version__)
1.0
1.6.0
1.0.5
3.2.2
1.19.2

But ​when I upgrade only the stream package to 1.1 I have the following error :

stream.filter_features(adata,min_n_cells = 5, assay = 'rna')
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/tmp/ipykernel_977625/1328372756.py in <module>
----> 1 st.filter_features(adata,min_n_cells = 5, assay = 'rna')

~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/stream/core.py in filter_features(adata, min_n_cells, max_n_cells, min_pct_cells, max_pct_cells, min_n_counts, max_n_counts, expr_cutoff, assay)
    627     else:
    628         n_counts = np.sum(adata.X,axis=0).astype(int)
--> 629         adata.var['n_counts'] = n_counts
    630     if('n_cells' in adata.var_keys()):
    631         n_cells = adata.var['n_cells']

~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in __setitem__(self, key, value)
   2936         else:
   2937             # set column
-> 2938             self._set_item(key, value)
   2939 
   2940     def _setitem_slice(self, key, value):

~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value)
   2998 
   2999         self._ensure_valid_index(value)
-> 3000         value = self._sanitize_column(key, value)
   3001         NDFrame._set_item(self, key, value)
   3002 

~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, key, value, broadcast)
   3634 
   3635             # turn me into an ndarray
-> 3636             value = sanitize_index(value, self.index, copy=False)
   3637             if not isinstance(value, (np.ndarray, Index)):
   3638                 if isinstance(value, list) and len(value) > 0:

~/miniconda3/envs/stream_1.1_ter/lib/python3.7/site-packages/pandas/core/internals/construction.py in sanitize_index(data, index, copy)
    609 
    610     if len(data) != len(index):
--> 611         raise ValueError("Length of values does not match length of index")
    612 
    613     if isinstance(data, ABCIndexClass) and not copy:

ValueError: Length of values does not match length of index

I also tried to create another conda environment by only fixing the version of STREAM :

print(stream.__version__)
print(scanpy.__version__)
print(pandas.__version__)
print(matplotlib.__version__)
print(numpy.__version__)
1.1
1.6.0
1.3.5
3.5.0
1.20.3

But I have about the same error when I run stream.filter_features(adata,min_n_cells = 5, assay = 'rna') :

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/tmp/ipykernel_978038/1328372756.py in <module>
----> 1 st.filter_features(adata,min_n_cells = 5, assay = 'rna')

~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/stream/core.py in filter_features(adata, min_n_cells, max_n_cells, min_pct_cells, max_pct_cells, min_n_counts, max_n_counts, expr_cutoff, assay)
    627     else:
    628         n_counts = np.sum(adata.X,axis=0).astype(int)
--> 629         adata.var['n_counts'] = n_counts
    630     if('n_cells' in adata.var_keys()):
    631         n_cells = adata.var['n_cells']

~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in __setitem__(self, key, value)
   3610         else:
   3611             # set column
-> 3612             self._set_item(key, value)
   3613 
   3614     def _setitem_slice(self, key: slice, value):

~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value)
   3782         ensure homogeneity.
   3783         """
-> 3784         value = self._sanitize_column(value)
   3785 
   3786         if (

~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, value)
   4507 
   4508         if is_list_like(value):
-> 4509             com.require_length_match(value, self.index)
   4510         return sanitize_array(value, self.index, copy=True, allow_2d=True)
   4511 

~/miniconda3/envs/stream_1.1_bis/lib/python3.7/site-packages/pandas/core/common.py in require_length_match(data, index)
    530     if len(data) != len(index):
    531         raise ValueError(
--> 532             "Length of values "
    533             f"({len(data)}) "
    534             "does not match length of index "

ValueError: Length of values (1) does not match length of index (32738)

And it's seems to be a numpy error but I am not very familiar with python...

What do you recommend for a functional STREAM 1.1 environment?

Best,
Lea

[huidongchen]

Hi thanks for letting us know. Instead of upgrading it to the latest version, can you install the latest version from scratch? This should help solve most of the incompatible package issues.

[tianchen2019]

Hi thanks for letting us know. Instead of upgrading it to the latest version, can you install the latest version from scratch? This should help solve most of the incompatible package issues.

i installed the latest version using the following code:
conda create -n stream python=3.7
conda activate stream
conda install -c bioconda stream

But, when i run

import stream as st 
adata=st.read(file_name='/outs/filtered_peak_bc_matrix/matrix.mtx',
file_sample='/outs/filtered_peak_bc_matrix/barcodes.tsv',
file_feature='/outs/filtered_peak_bc_matrix/peaks.bed',
file_format='mtx',workdir='./result_atac')
adata.var.index =adata.var[0].astype(str) + '' + adata.var[1].astype(str) +'' + adata.var[2].astype(str)
st.cal_qc(adata2,assay='atac')

the error is

ValueError Traceback (most recent call last)
/tmp/ipykernel_352024/3261032759.py in
----> 1 st.cal_qc(adata,assay='atac')

~/app/ENTER/envs/stream1/lib/python3.7/site-packages/stream/core.py in cal_qc(adata, expr_cutoff, assay)
438
439 n_counts = adata.X.sum(axis=0)
--> 440 adata.var['n_counts'] = n_counts
441 n_cells = (adata.X>=expr_cutoff).sum(axis=0)
442 adata.var['n_cells'] = n_cells

~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in setitem(self, key, value)
3610 else:
3611 # set column
-> 3612 self._set_item(key, value)
3613
3614 def _setitem_slice(self, key: slice, value):

~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in _set_item(self, key, value)
3782 ensure homogeneity.
3783 """
-> 3784 value = self._sanitize_column(value)
3785
3786 if (

~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/frame.py in _sanitize_column(self, value)
4507
4508 if is_list_like(value):
-> 4509 com.require_length_match(value, self.index)
4510 return sanitize_array(value, self.index, copy=True, allow_2d=True)
4511

~/app/ENTER/envs/stream1/lib/python3.7/site-packages/pandas/core/common.py in require_length_match(data, index)
530 if len(data) != len(index):
531 raise ValueError(
--> 532 "Length of values "
533 f"({len(data)}) "
534 "does not match length of index "

ValueError: Length of values (1) does not match length of index (156605)

my package version is

stream=1.1
pandas=1.3.5
numpy=1.21.5

[bellenger-l]

Hello,

I managed to look a lit bit further this issue by testing my script with the STREAM dataset. It working pretty fine and I understood that it is because of the input format. What I don't understand why but when you use the 3 files format (or format = 'mtx') it end with the issue that @tianchen2019 and I mentioned.

In fact the format of adata.X change.

With my data in 3 files format I have :

print(adata.X)
[240 rows x 2 columns]
  (0, 1)	1.0
  (0, 5)	1.0
  (0, 8)	3.0
  (0, 11)	1.0
  (0, 22)	1.0
...

When with the tsv file of Nestorowa dataset :

print(adata.X)
[4768 rows x 0 columns]
[[0.         4.8916044  1.4261482  ... 1.4261482  0.         7.869409  ]
 [0.         6.8777246  0.         ... 0.         0.         0.        ]
 [0.         0.         6.9133844  ... 2.0516593  0.         1.3634025 ]
 ...
 [0.         1.2770978  0.         ... 0.         0.         0.77547604]
 [0.         1.878352   0.         ... 0.         0.         0.        ]
 [0.         3.3741634  0.         ... 0.         0.         0.        ]]

So I tried this dataset with 3 files format (that end up with the same error as described in this issue) :

print(adata.X)
[4768 rows x 2 columns]
  (0, 1)	4.8916044
  (0, 2)	1.4261482
  (0, 5)	2.599758
  (0, 6)	2.9540346
  (0, 7)	6.3573685
  (0, 8)	2.12914
  (0, 9)	1.4261482
...

And finally I tried to change my dataset into a tsv format where I have :

print(adata.X)
[240 rows x 0 columns]
[[0. 1. 0. ... 1. 0. 0.]
 [0. 0. 0. ... 0. 1. 0.]
 [0. 0. 0. ... 0. 0. 0.]
 ...
 [0. 0. 0. ... 0. 0. 0.]
 [0. 0. 0. ... 0. 0. 0.]
 [0. 0. 0. ... 0. 0. 0.]]

So it's the same shape as the Nestorowa dataset in tsv but when I follow my script I end up with no variable feature where STREAM 1.0 succeed to detect 230 variable features...

Still stuck at this moment and I don't know why... For the time being I continue to use the version 1.0

Best,
Lea

[bellenger-l]

Hello @huidongchen,

I didn't succeed to upgrade and use STREAM v1.1. Would it be possible to provide the command line to install STREAM 1.1 with the dependency versions ? Like what you gave for STREAM 1.0 :

conda create -n env_stream python=3.7 stream=1.0 jupyter

Including the version for pandas, numpy, matplotlib ?

This would be greatly appreciated
Best regards,
Lea

[huidongchen]

Hi Lea, thanks for the feedback. Unfortunately It's not really trivial to figure out all the dependencies that are compatible with the old STREAM v1.0.. I would strongly recommend using the latest version.

As I suggested before, instead of upgrading stream from v1.0 to v1.1, can you try to install stream v1.1 from scratch with the code below:

conda create -n env_stream python=3.7 stream=1.1 jupyter
conda activate env_stream

The issue @tianchen2019 described is related to scATAC-seq analysis. I need to look further into that. but v1.1 should work fine with scRNA-seq data.

[bellenger-l]

Hello @huidongchen ! Sorry for the delay I had multiple problems with conda so it took time for me to create another environnement.

Unfortunately I had the same issue. Here is the conda list :

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
_r-mutex                  1.0.0               anacondar_1    r
_sysroot_linux-64_curr_repodata_hack 3                   haa98f57_10  
anndata                   0.6.22.post1               py_0    bioconda
anyio                     3.5.0            py37h06a4308_0  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0           py37h7f8727e_0  
arpack                    3.7.0                hc6cf775_2    conda-forge
attrs                     22.1.0           py37h06a4308_0  
backcall                  0.2.0              pyhd3eb1b0_0  
beautifulsoup4            4.11.1           py37h06a4308_0  
binutils_impl_linux-64    2.35.1               h27ae35d_9  
binutils_linux-64         2.35.1              h454624a_30  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd3eb1b0_0  
blosc                     1.21.3               h6a678d5_0  
bottleneck                1.3.5            py37h7deecbd_0  
brotli                    1.0.9                h5eee18b_7  
brotli-bin                1.0.9                h5eee18b_7  
bwidget                   1.9.11                        1  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2023.01.10           h06a4308_0  
cairo                     1.16.0               hb05425b_3  
certifi                   2022.12.7        py37h06a4308_0  
cffi                      1.15.1           py37h5eee18b_3  
colorama                  0.4.6            py37h06a4308_0  
curl                      7.69.1               hbc83047_0  
cycler                    0.11.0             pyhd3eb1b0_0  
dbus                      1.13.18              hb2f20db_0  
debugpy                   1.5.1            py37h295c915_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
dunamai                   1.16.0             pyhd8ed1ab_0    conda-forge
entrypoints               0.4              py37h06a4308_0  
expat                     2.4.9                h6a678d5_0  
flit-core                 3.6.0              pyhd3eb1b0_0  
fontconfig                2.14.1               h52c9d5c_1  
fonttools                 4.25.0             pyhd3eb1b0_0  
freetype                  2.12.1               h4a9f257_0  
fribidi                   1.0.10               h7b6447c_0  
gcc_impl_linux-64         7.5.0               h7105cf2_17  
gcc_linux-64              7.5.0               h8f34230_30  
gdbm                      1.18                 hd4cb3f1_4  
geos                      3.8.0                he6710b0_0  
get_version               3.5.4              pyhd8ed1ab_0    conda-forge
gettext                   0.21.0               hf68c758_0  
gfortran_impl_linux-64    7.5.0               ha8c8e06_17  
gfortran_linux-64         7.5.0               h96bb648_30  
giflib                    5.2.1                h5eee18b_1  
git                       2.32.0          pl5262hc120c5b_1  
glib                      2.69.1               he621ea3_2  
glpk                      4.65                 h276157c_3  
gmp                       6.2.1                h295c915_3  
graphite2                 1.3.14               h295c915_1  
gsl                       2.4                  h14c3975_4  
gst-plugins-base          1.14.1               h6a678d5_1  
gstreamer                 1.14.1               h5eee18b_1  
gunicorn                  20.1.0           py37h06a4308_0  
gxx_impl_linux-64         7.5.0               h0a5bf11_17  
gxx_linux-64              7.5.0               hffc177d_30  
h5py                      3.7.0            py37h737f45e_0  
harfbuzz                  4.3.0                hd55b92a_0  
hdf5                      1.10.6               hb1b8bf9_0  
icu                       58.2                 he6710b0_3  
idna                      3.4              py37h06a4308_0  
igraph                    0.9.8                hf5496dd_0    conda-forge
importlib-metadata        4.11.3           py37h06a4308_0  
importlib_metadata        4.11.3               hd3eb1b0_0  
importlib_resources       5.2.0              pyhd3eb1b0_1  
intel-openmp              2021.4.0          h06a4308_3561  
ipykernel                 6.15.2           py37h06a4308_0  
ipython                   7.31.1           py37h06a4308_1  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
jedi                      0.18.1           py37h06a4308_1  
jinja2                    3.1.2            py37h06a4308_0  
joblib                    1.1.1            py37h06a4308_0  
jpeg                      9e                   h7f8727e_0  
jsonschema                4.17.3           py37h06a4308_0  
jupyter_client            7.4.9            py37h06a4308_0  
jupyter_core              4.11.2           py37h06a4308_0  
jupyter_server            1.23.4           py37h06a4308_0  
jupyterlab_pygments       0.1.2                      py_0  
kernel-headers_linux-64   3.10.0              h57e8cba_10  
kiwisolver                1.4.4            py37h6a678d5_0  
krb5                      1.17.1               h173b8e3_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.35.1               h7274673_9  
legacy-api-wrap           1.2                        py_0    conda-forge
lerc                      3.0                  h295c915_0  
libblas                   3.9.0            12_linux64_mkl    conda-forge
libbrotlicommon           1.0.9                h5eee18b_7  
libbrotlidec              1.0.9                h5eee18b_7  
libbrotlienc              1.0.9                h5eee18b_7  
libcurl                   7.69.1               h20c2e04_0  
libdeflate                1.8                  h7f8727e_5  
libedit                   3.1.20221030         h5eee18b_0  
libffi                    3.4.2                h6a678d5_6  
libgcc-devel_linux-64     7.5.0               hbbeae57_17  
libgcc-ng                 11.2.0               h1234567_1  
libgfortran-ng            7.5.0               ha8ba4b0_17  
libgfortran4              7.5.0               ha8ba4b0_17  
libgomp                   11.2.0               h1234567_1  
libiconv                  1.16                 h7f8727e_2  
liblapack                 3.9.0            12_linux64_mkl    conda-forge
libllvm11                 11.1.0               h9e868ea_6  
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.18               h7b6447c_0  
libssh2                   1.10.0               h8f2d780_0  
libstdcxx-devel_linux-64  7.5.0               hf0c5c8d_17  
libstdcxx-ng              11.2.0               h1234567_1  
libtiff                   4.5.0                h6a678d5_1  
libuuid                   1.41.5               h5eee18b_0  
libwebp                   1.2.4                h11a3e52_0  
libwebp-base              1.2.4                h5eee18b_0  
libxcb                    1.15                 h7f8727e_0  
libxml2                   2.9.14               h74e7548_0  
libxslt                   1.1.35               h4e12654_0  
llvmlite                  0.39.1           py37he621ea3_0  
louvain                   0.7.1            py37hd23a5d3_2    conda-forge
lxml                      4.9.1            py37h1edc446_0  
lz4-c                     1.9.4                h6a678d5_0  
lzo                       2.10                 h7b6447c_2  
make                      4.2.1                h1bed415_1  
markupsafe                2.1.1            py37h7f8727e_0  
matplotlib                3.5.3            py37h06a4308_0  
matplotlib-base           3.5.3            py37hf590b9c_0  
matplotlib-inline         0.1.6            py37h06a4308_0  
metis                     5.1.0                hf484d3e_4  
mistune                   0.8.4           py37h14c3975_1001  
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py37h7f8727e_0  
mkl_fft                   1.3.1            py37hd3c417c_0  
mkl_random                1.2.2            py37h51133e4_0  
mock                      4.0.3              pyhd3eb1b0_0  
mpfr                      4.0.2                hb69a4c5_1  
munkres                   1.1.4                      py_0  
natsort                   7.1.1              pyhd3eb1b0_0  
nbclassic                 0.4.8            py37h06a4308_0  
nbclient                  0.5.13           py37h06a4308_0  
nbconvert                 6.5.4            py37h06a4308_0  
nbformat                  5.7.0            py37h06a4308_0  
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.5.6            py37h06a4308_0  
networkx                  2.1                      py37_0  
notebook                  6.5.2            py37h06a4308_0  
notebook-shim             0.2.2            py37h06a4308_0  
numba                     0.56.4           py37h417a72b_0  
numexpr                   2.8.4            py37he184ba9_0  
numpy                     1.21.5           py37h6c91a56_3  
numpy-base                1.21.5           py37ha15fc14_3  
openssl                   1.1.1t               h7f8727e_0  
packaging                 22.0             py37h06a4308_0  
pandas                    1.3.5            py37h8c16a72_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
pango                     1.50.7               h05da053_0  
parso                     0.8.3              pyhd3eb1b0_0  
patsy                     0.5.3            py37h06a4308_0  
pcre                      8.45                 h295c915_0  
pcre2                     10.35                h14c3975_1  
perl                      5.34.0               h5eee18b_2  
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    9.3.0            py37h6a678d5_2  
pip                       22.3.1           py37h06a4308_0  
pixman                    0.40.0               h7f8727e_1  
pkgutil-resolve-name      1.3.10           py37h06a4308_0  
plotly                    5.9.0            py37h06a4308_0  
prometheus_client         0.14.1           py37h06a4308_0  
prompt-toolkit            3.0.36           py37h06a4308_0  
psutil                    5.9.0            py37h5eee18b_0  
ptyprocess                0.7.0              pyhd3eb1b0_2  
pycparser                 2.21               pyhd3eb1b0_0  
pygments                  2.11.2             pyhd3eb1b0_0  
pynndescent               0.5.4              pyhd3eb1b0_0  
pyparsing                 3.0.9            py37h06a4308_0  
pyqt                      5.9.2            py37h05f1152_2  
pyrsistent                0.18.0           py37heee7806_0  
pytables                  3.7.0            py37hf19a122_1  
python                    3.7.16               h7a1cb2a_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-fastjsonschema     2.16.2           py37h06a4308_0  
python-igraph             0.9.10           py37h48d2a39_0    conda-forge
python-slugify            5.0.2              pyhd3eb1b0_0  
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2022.7           py37h06a4308_0  
pyzmq                     23.2.0           py37h6a678d5_0  
qt                        5.9.7                h5867ecd_1  
r-askpass                 1.0               r36h14c3975_0    r
r-assertthat              0.2.1             r36h6115d3f_0    r
r-backports               1.1.4             r36h96ca727_0    r
r-base                    3.6.1                haffb61f_2    r
r-base64enc               0.1_3             r36h96ca727_4    r
r-bh                      1.69.0_1          r36h6115d3f_0    r
r-bit                     1.1_14            r36h96ca727_0    r
r-bit64                   0.9_7             r36h96ca727_0    r
r-blob                    1.1.1             r36h6115d3f_0    r
r-boot                    1.3_20            r36h6115d3f_0    r
r-broom                   0.5.2             r36h6115d3f_0    r
r-callr                   3.2.0             r36h6115d3f_0    r
r-caret                   6.0_83            r36h96ca727_0    r
r-cellranger              1.1.0             r36h6115d3f_0    r
r-class                   7.3_15            r36h96ca727_0    r
r-cli                     1.1.0             r36h6115d3f_0    r
r-clipr                   0.6.0             r36h6115d3f_0    r
r-clisymbols              1.2.0             r36h6115d3f_0    r
r-cluster                 2.0.8             r36ha65eedd_0    r
r-codetools               0.2_16            r36h6115d3f_0    r
r-colorspace              1.4_1             r36h96ca727_0    r
r-cowplot                 1.1.1             r36hc72bb7e_0    conda-forge
r-crayon                  1.3.4             r36h6115d3f_0    r
r-curl                    3.3               r36h96ca727_0    r
r-data.table              1.12.2            r36h96ca727_0    r
r-dbi                     1.0.0             r36h6115d3f_0    r
r-dbplyr                  1.4.0             r36h6115d3f_0    r
r-desc                    1.2.0             r36h6115d3f_0    r
r-devtools                2.0.2             r36h6115d3f_0    r
r-dichromat               2.0_0             r36h6115d3f_4    r
r-digest                  0.6.18            r36h96ca727_0    r
r-distutils               1.0             r36h516909a_1003    conda-forge
r-dplyr                   0.8.0.1           r36h29659fb_0    r
r-ellipsis                0.1.0             r36h96ca727_0    r
r-elpigraph.r             1.0.0           r36h516909a_1003    conda-forge
r-essentials              3.6.0                     r36_0    r
r-evaluate                0.13              r36h6115d3f_0    r
r-fansi                   0.4.0             r36h96ca727_0    r
r-farver                  1.1.0             r36h29659fb_0    r
r-forcats                 0.4.0             r36h6115d3f_0    r
r-foreach                 1.4.4             r36h6115d3f_0    r
r-foreign                 0.8_71            r36h96ca727_0    r
r-formatr                 1.6               r36h6115d3f_0    r
r-fs                      1.2.7             r36h29659fb_0    r
r-generics                0.0.2             r36h6115d3f_0    r
r-gensa                   1.1.7             r36h29659fb_0    r
r-ggforce                 0.3.3             r36h03ef668_0    conda-forge
r-ggplot2                 3.1.1             r36h6115d3f_0    r
r-ggpubr                  0.2.5             r36h6115d3f_1    conda-forge
r-ggrepel                 0.9.1             r36h03ef668_0    conda-forge
r-ggsci                   2.9             r36h6115d3f_1003    conda-forge
r-ggsignif                0.6.1             r36hc72bb7e_0    conda-forge
r-gh                      1.0.1             r36h6115d3f_0    r
r-git2r                   0.25.2            r36h96ca727_0    r
r-glmnet                  2.0_16            r36ha65eedd_0    r
r-glue                    1.3.1             r36h96ca727_0    r
r-gower                   0.2.0             r36h96ca727_0    r
r-gridextra               2.3               r36h6115d3f_0    r
r-gtable                  0.3.0             r36h6115d3f_0    r
r-haven                   2.1.0             r36h29659fb_0    r
r-hexbin                  1.27.2            r36ha65eedd_0    r
r-highr                   0.8               r36h6115d3f_0    r
r-hms                     0.4.2             r36h6115d3f_0    r
r-htmltools               0.3.6             r36h29659fb_0    r
r-htmlwidgets             1.3               r36h6115d3f_0    r
r-httpuv                  1.5.1             r36h29659fb_0    r
r-httr                    1.4.0             r36h6115d3f_0    r
r-igraph                  1.2.4.1           r36h80f5a37_0    r
r-infotheo                1.2.0             r36h29659fb_0    r
r-ini                     0.3.1             r36h6115d3f_0    r
r-ipred                   0.9_8             r36h96ca727_0    r
r-irdisplay               0.7.0             r36h6115d3f_0    r
r-irkernel                0.8.15                    r36_0    r
r-irlba                   2.3.3             r36h96ca727_0    r
r-iterators               1.0.10            r36h6115d3f_0    r
r-jsonlite                1.6               r36h96ca727_0    r
r-kernsmooth              2.23_15           r36ha65eedd_4    r
r-knitr                   1.22              r36h6115d3f_0    r
r-labeling                0.3               r36h6115d3f_4    r
r-later                   0.8.0             r36h29659fb_0    r
r-lattice                 0.20_38           r36h96ca727_0    r
r-lava                    1.6.5             r36h6115d3f_0    r
r-lazyeval                0.2.2             r36h96ca727_0    r
r-lubridate               1.7.4             r36h29659fb_0    r
r-magrittr                1.5               r36h6115d3f_4    r
r-maps                    3.3.0             r36h96ca727_0    r
r-markdown                0.9               r36h96ca727_0    r
r-mass                    7.3_51.3          r36h96ca727_0    r
r-matrix                  1.2_17            r36h96ca727_0    r
r-memoise                 1.1.0             r36h6115d3f_0    r
r-mgcv                    1.8_28            r36h96ca727_0    r
r-mime                    0.6               r36h96ca727_0    r
r-modelmetrics            1.2.2             r36h29659fb_0    r
r-modelr                  0.1.4             r36h6115d3f_0    r
r-munsell                 0.5.0             r36h6115d3f_0    r
r-nlme                    3.1_139           r36ha65eedd_0    r
r-nnet                    7.3_12            r36h96ca727_0    r
r-numderiv                2016.8_1          r36h6115d3f_0    r
r-openssl                 1.3               r36h96ca727_0    r
r-pbdzmq                  0.3_3             r36h5455479_1    r
r-pillar                  1.3.1             r36h6115d3f_0    r
r-pkgbuild                1.0.3             r36h6115d3f_0    r
r-pkgconfig               2.0.2             r36h6115d3f_0    r
r-pkgload                 1.0.2             r36h29659fb_0    r
r-plogr                   0.2.0             r36h6115d3f_0    r
r-plyr                    1.8.4             r36h29659fb_0    r
r-polyclip                1.10_0            r36h29659fb_0    r
r-polynom                 1.4_0             r36h6115d3f_0    r
r-prettyunits             1.0.2             r36h6115d3f_0    r
r-processx                3.3.0             r36h96ca727_0    r
r-prodlim                 2018.04.18        r36h29659fb_0    r
r-progress                1.2.0             r36h6115d3f_0    r
r-promises                1.0.1             r36h29659fb_0    r
r-ps                      1.3.0             r36h96ca727_0    r
r-purrr                   0.3.2             r36h96ca727_0    r
r-quantmod                0.4_14            r36h6115d3f_0    r
r-r6                      2.4.0             r36h6115d3f_0    r
r-randomforest            4.6_14            r36ha65eedd_0    r
r-rbokeh                  0.6.3                     r36_0    r
r-rcmdcheck               1.3.2             r36h6115d3f_0    r
r-rcolorbrewer            1.1_2             r36h6115d3f_0    r
r-rcpp                    1.0.1             r36h29659fb_0    r
r-rcpparmadillo           0.9.300.2.0       r36h29659fb_0    r
r-rcppeigen               0.3.3.5.0         r36h29659fb_0    r
r-rcpproll                0.3.0             r36h29659fb_0    r
r-readr                   1.3.1             r36h29659fb_0    r
r-readxl                  1.3.1             r36h29659fb_0    r
r-recipes                 0.1.5             r36h6115d3f_0    r
r-recommended             3.6.0                     r36_0    r
r-rematch                 1.0.1             r36h6115d3f_0    r
r-remotes                 2.0.4             r36h6115d3f_0    r
r-repr                    0.19.2            r36h6115d3f_0    r
r-reprex                  0.2.1             r36h6115d3f_0    r
r-reshape2                1.4.3             r36h29659fb_0    r
r-rlang                   0.3.4             r36h96ca727_0    r
r-rmarkdown               1.12              r36h6115d3f_0    r
r-rpart                   4.1_15            r36h96ca727_0    r
r-rprojroot               1.3_2             r36h6115d3f_0    r
r-rsqlite                 2.1.1             r36h29659fb_0    r
r-rstudioapi              0.10              r36h6115d3f_0    r
r-rvest                   0.3.3             r36h6115d3f_0    r
r-scales                  1.0.0             r36h29659fb_0    r
r-segmented               1.0_0             r36h6115d3f_0    r
r-selectr                 0.4_1             r36h6115d3f_0    r
r-sessioninfo             1.1.1             r36h6115d3f_0    r
r-shiny                   1.3.2             r36h6115d3f_0    r
r-sourcetools             0.1.7             r36h29659fb_0    r
r-spatial                 7.3_11            r36h96ca727_4    r
r-squarem                 2017.10_1         r36h6115d3f_0    r
r-stringi                 1.4.3             r36h29659fb_0    r
r-stringr                 1.4.0             r36h6115d3f_0    r
r-survival                2.44_1.1          r36h96ca727_0    r
r-sys                     3.2               r36h96ca727_0    r
r-tibble                  2.1.1             r36h96ca727_0    r
r-tictoc                  1.0               r36h6115d3f_0    r
r-tidyr                   0.8.3             r36h29659fb_0    r
r-tidyselect              0.2.5             r36h29659fb_0    r
r-tidyverse               1.2.1             r36h6115d3f_0    r
r-timedate                3043.102          r36h6115d3f_0    r
r-tinytex                 0.12              r36h6115d3f_0    r
r-ttr                     0.23_4            r36ha65eedd_0    r
r-tweenr                  1.0.2             r36h03ef668_0    conda-forge
r-usethis                 1.5.0             r36h6115d3f_0    r
r-utf8                    1.1.4             r36h96ca727_0    r
r-uuid                    0.1_2             r36h96ca727_4    r
r-vgam                    1.1_1             r36ha65eedd_0    r
r-viridislite             0.3.0             r36h6115d3f_0    r
r-whisker                 0.3_2             r36h6115d3f_4    r
r-withr                   2.1.2             r36h6115d3f_0    r
r-xfun                    0.6               r36h6115d3f_0    r
r-xml                     3.98_1.19         r36h96ca727_0    r
r-xml2                    1.2.0             r36h29659fb_0    r
r-xopen                   1.0.0             r36h6115d3f_0    r
r-xtable                  1.8_4             r36h6115d3f_0    r
r-xts                     0.11_2            r36h96ca727_0    r
r-yaml                    2.2.0             r36h96ca727_0    r
r-zoo                     1.8_6             r36h96ca727_0    r
readline                  8.2                  h5eee18b_0  
rpy2                      2.9.4           py37r36hd767a1f_3    conda-forge
scanpy                    1.4.4.post1                py_0    bioconda
scikit-learn              1.0.2            py37h51133e4_1  
scipy                     1.7.3            py37hc147768_0  
seaborn                   0.12.2           py37h06a4308_0  
send2trash                1.8.0              pyhd3eb1b0_1  
setuptools                65.6.3           py37h06a4308_0  
setuptools-scm            7.0.4            py37h06a4308_0  
setuptools_scm            7.0.4                hd3eb1b0_0  
shapely                   1.8.4            py37h81ba7c5_0  
simplegeneric             0.8.1                    py37_2  
sinfo                     0.3.1                      py_0    conda-forge
sip                       4.19.8           py37hf484d3e_0  
six                       1.16.0             pyhd3eb1b0_1  
sniffio                   1.2.0            py37h06a4308_1  
soupsieve                 2.3.2.post1      py37h06a4308_0  
sqlite                    3.40.1               h5082296_0  
statsmodels               0.13.5           py37h7deecbd_0  
stdlib-list               0.8.0            py37h06a4308_0  
stream                    1.1                pyhdfd78af_0    bioconda
suitesparse               5.10.1               h446ee2e_2  
sysroot_linux-64          2.17                h57e8cba_10  
tbb                       2021.6.0             hdb19cb5_1  
tenacity                  8.0.1            py37h06a4308_1  
terminado                 0.17.1           py37h06a4308_0  
text-unidecode            1.3                pyhd3eb1b0_0  
texttable                 1.6.4              pyhd3eb1b0_0  
threadpoolctl             2.2.0              pyh0d69192_0  
tinycss2                  1.2.1            py37h06a4308_0  
tk                        8.6.12               h1ccaba5_0  
tktable                   2.10                 h14c3975_0  
tomli                     2.0.1            py37h06a4308_0  
tornado                   6.2              py37h5eee18b_0  
tqdm                      4.64.1           py37h06a4308_0  
traitlets                 5.7.1            py37h06a4308_0  
typing-extensions         4.4.0            py37h06a4308_0  
typing_extensions         4.4.0            py37h06a4308_0  
tzlocal                   2.1              py37h06a4308_1  
umap-learn                0.5.3            py37h89c1867_0    conda-forge
unidecode                 1.2.0              pyhd3eb1b0_0  
unzip                     6.0                  h611a1e1_0  
wcwidth                   0.2.5              pyhd3eb1b0_0  
webencodings              0.5.1                    py37_1  
websocket-client          0.58.0           py37h06a4308_4  
wheel                     0.38.4           py37h06a4308_0  
xz                        5.2.10               h5eee18b_1  
zeromq                    4.3.4                h2531618_0  
zip                       3.0                  h7f8727e_1  
zipp                      3.11.0           py37h06a4308_0  
zlib                      1.2.13               h5eee18b_0  
zstd                      1.5.2                ha4553b6_0  

And here is the conda info :

     active environment : stream_mamba
    active env location : /home/lea/miniconda3/envs/stream_mamba
            shell level : 1
       user config file : /home/lea/.condarc
 populated config files : /home/lea/.condarc
          conda version : 23.1.0
    conda-build version : 3.23.3
         python version : 3.10.9.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.31=0
                          __linux=5.4.0=0
                          __unix=0=0
       base environment : /home/lea/miniconda3  (writable)
      conda av data dir : /home/lea/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/lea/miniconda3/pkgs
                          /home/lea/.conda/pkgs
       envs directories : /home/lea/miniconda3/envs
                          /home/lea/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.4.0-139-generic ubuntu/20.04.6 glibc/2.31
                UID:GID : 1005:1005
             netrc file : None
           offline mode : False

As I described in my previous messages, all the environments in stream 1.1 don't work when we import our data in the bundle format (mtx). The structure of the expression matrix change and it seems cause the following error while running select_variable_genes :

---------------------------------------------------------------------------
AxisError                                 Traceback (most recent call last)
/tmp/ipykernel_1515188/1347598060.py in <module>
      1 ### Highly variable genes
----> 2 stream.select_variable_genes(Int_5CT_adata,loess_frac=0.01,percentile=95)
      3 Int_5CT_adata.uns['var_genes_selected'] = Int_5CT_adata.uns['var_genes'] #keep the information in another slot if needed

/home/lea/miniconda3/envs/stream_mamba/lib/python3.7/site-packages/stream/core.py in select_variable_genes(adata, loess_frac, percentile, n_genes, n_jobs, save_fig, fig_name, fig_path, fig_size, pad, w_pad, h_pad)
    900     fig_size = mpl.rcParams['figure.figsize'] if fig_size is None else fig_size
    901     mean_genes = np.mean(adata.X,axis=0)
--> 902     std_genes = np.std(adata.X,ddof=1,axis=0)
    903     loess_fitted = lowess(std_genes,mean_genes,return_sorted=False,frac=loess_frac)
    904     residuals = std_genes - loess_fitted

<__array_function__ internals> in std(*args, **kwargs)

/home/lea/miniconda3/envs/stream_mamba/lib/python3.7/site-packages/numpy/core/fromnumeric.py in std(a, axis, dtype, out, ddof, keepdims, where)
   3580 
   3581     return _methods._std(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
-> 3582                          **kwargs)
   3583 
   3584 

/home/lea/miniconda3/envs/stream_mamba/lib/python3.7/site-packages/numpy/core/_methods.py in _std(a, axis, dtype, out, ddof, keepdims, where)
    261          where=True):
    262     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
--> 263                keepdims=keepdims, where=where)
    264 
    265     if isinstance(ret, mu.ndarray):

/home/lea/miniconda3/envs/stream_mamba/lib/python3.7/site-packages/numpy/core/_methods.py in _var(a, axis, dtype, out, ddof, keepdims, where)
    197     arr = asanyarray(a)
    198 
--> 199     rcount = _count_reduce_items(arr, axis, keepdims=keepdims, where=where)
    200     # Make this warning show up on top.
    201     if ddof >= rcount if where is True else umr_any(ddof >= rcount, axis=None):

/home/lea/miniconda3/envs/stream_mamba/lib/python3.7/site-packages/numpy/core/_methods.py in _count_reduce_items(arr, axis, keepdims, where)
     74         items = nt.intp(1)
     75         for ax in axis:
---> 76             items *= arr.shape[mu.normalize_axis_index(ax, arr.ndim)]
     77     else:
     78         # TODO: Optimize case when `where` is broadcast along a non-reduction

AxisError: axis 0 is out of bounds for array of dimension 0

The structure of adata.X in stream 1.1 is :

<24570x2000 sparse matrix of type '<class 'numpy.float32'>'
	with 6980887 stored elements in Compressed Sparse Row format>

But in stream 1.0 (where everything is fine) the structure is :

array([[ 0.        ,  0.        ,  0.        , ...,  0.        ,
         0.        ,  0.        ],
       [ 0.        ,  0.        ,  0.        , ...,  0.        ,
         0.        ,  0.        ],
       [ 0.        ,  0.        ,  0.        , ...,  0.        ,
         0.        ,  0.        ],
       ...,
       [-0.39902183, -0.03658423,  0.        , ...,  0.        ,
         0.        ,  0.        ],
       [ 0.        , -0.04271474,  0.        , ...,  0.        ,
         0.        ,  0.        ],
       [ 0.00093189, -0.22098285, -0.1300799 , ...,  0.        ,
         0.        ,  0.        ]], dtype=float32)

Here is the conda list for the environment 1.0 :

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_r-mutex                  1.0.0               anacondar_1  
alabaster                 0.7.12             pyhd3eb1b0_0  
anndata                   0.7.8            py37h89c1867_1    conda-forge
argon2-cffi               20.1.0           py37h27cfd23_1  
async_generator           1.10               pyhd3eb1b0_0  
attrs                     20.3.0             pyhd3eb1b0_0  
babel                     2.9.1              pyhd3eb1b0_0  
backcall                  0.2.0              pyhd3eb1b0_0  
binutils_impl_linux-64    2.33.1               he6710b0_7  
binutils_linux-64         2.33.1              h9595d00_15  
blas                      1.0                         mkl  
bleach                    3.3.0              pyhd3eb1b0_0  
blosc                     1.21.0               h8c45485_0  
brotlipy                  0.7.0           py37h27cfd23_1003  
bwidget                   1.9.11                        1  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2021.10.26           h06a4308_2  
cairo                     1.14.12              h8948797_3  
certifi                   2021.10.8        py37h06a4308_2  
cffi                      1.14.5           py37h261ae71_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
colorama                  0.4.4              pyhd3eb1b0_0  
cryptography              36.0.0           py37h9ce1e76_0  
curl                      7.69.1               hbc83047_0  
cycler                    0.10.0                   py37_0  
dbus                      1.13.18              hb2f20db_0  
decorator                 4.4.2              pyhd3eb1b0_0  
defusedxml                0.6.0              pyhd3eb1b0_0  
docutils                  0.17.1           py37h06a4308_1  
dunamai                   1.5.5              pyhd8ed1ab_0    conda-forge
entrypoints               0.3                      py37_0  
expat                     2.2.10               he6710b0_2  
fontconfig                2.13.1               h6c09931_0  
freetype                  2.10.4               h5ab3b9f_0  
fribidi                   1.0.10               h7b6447c_0  
gcc_impl_linux-64         7.3.0                habb00fd_1  
gcc_linux-64              7.3.0               h553295d_15  
geos                      3.8.0                he6710b0_0  
get_version               3.5                pyhd8ed1ab_0    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1  
gfortran_linux-64         7.3.0               h553295d_15  
glib                      2.67.3               h36276a3_1  
graphite2                 1.3.14               h23475e2_0  
gsl                       2.4                  h14c3975_4  
gst-plugins-base          1.14.0               h8213a91_2  
gstreamer                 1.14.0               h28cd5cc_2  
gunicorn                  20.0.4                   py37_0  
gxx_impl_linux-64         7.3.0                hdf63c60_1  
gxx_linux-64              7.3.0               h553295d_15  
h5py                      2.10.0           py37hd6299e0_1  
harfbuzz                  2.4.0                hca77d97_1  
hdf5                      1.10.6               hb1b8bf9_0  
icu                       58.2                 he6710b0_3  
idna                      3.3                pyhd3eb1b0_0  
imagesize                 1.3.0              pyhd3eb1b0_0  
importlib-metadata        2.0.0                      py_1  
importlib_metadata        2.0.0                         1  
intel-openmp              2020.2                      254  
ipykernel                 5.3.4            py37h5ca1d4c_0  
ipython                   7.20.0           py37hb070fc8_1  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.6.3              pyhd3eb1b0_1  
jedi                      0.17.2           py37h06a4308_1  
jinja2                    2.11.3             pyhd3eb1b0_0  
joblib                    1.0.0              pyhd3eb1b0_0  
jpeg                      9b                   h024ee3a_2  
jsonschema                3.2.0                      py_2  
jupyter                   1.0.0                    py37_7  
jupyter_client            6.1.7                      py_0  
jupyter_console           6.2.0                      py_0  
jupyter_core              4.7.1            py37h06a4308_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
kiwisolver                1.3.1            py37h2531618_0  
krb5                      1.17.1               h173b8e3_0  
ld_impl_linux-64          2.33.1               h53a641e_7  
legacy-api-wrap           1.2                        py_0    conda-forge
libcurl                   7.69.1               h20c2e04_0  
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
libllvm10                 10.0.1               hbcb73fb_5  
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.18               h7b6447c_0  
libssh2                   1.9.0                h1ba5d50_1  
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.1.0                h2733197_1  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.10               hb55368b_3  
llvmlite                  0.34.0           py37h269e1b5_4  
lz4-c                     1.9.3                h2531618_0  
lzo                       2.10                 h7b6447c_2  
make                      4.2.1                h1bed415_1  
markupsafe                1.1.1            py37h14c3975_1  
matplotlib                3.2.2                         0  
matplotlib-base           3.2.2            py37hef1b27d_0  
mistune                   0.8.4           py37h14c3975_1001  
mkl                       2020.2                      256  
mkl-service               2.3.0            py37he8ac12f_0  
mkl_fft                   1.2.0            py37h23d657b_0  
mkl_random                1.1.1            py37h0573a6f_0  
mock                      4.0.3              pyhd3eb1b0_0  
natsort                   7.1.1              pyhd3eb1b0_0  
nbclient                  0.5.1                      py_0  
nbconvert                 6.0.7                    py37_0  
nbformat                  5.1.2              pyhd3eb1b0_1  
ncurses                   6.2                  he6710b0_1  
nest-asyncio              1.4.3              pyhd3eb1b0_0  
networkx                  2.1                      py37_0  
notebook                  6.2.0            py37h06a4308_0  
numba                     0.51.2           py37h04863e7_1  
numexpr                   2.7.3            py37hb2eb853_0  
numpy                     1.19.2           py37h54aff64_0  
numpy-base                1.19.2           py37hfa32c7d_0  
openssl                   1.1.1m               h7f8727e_0  
packaging                 20.9               pyhd3eb1b0_0  
pandas                    1.0.5            py37h0573a6f_0  
pandoc                    2.11                 hb0f4dca_0  
pandocfilters             1.4.3            py37h06a4308_1  
pango                     1.45.3               hd140c19_0  
parso                     0.7.0                      py_0  
patsy                     0.5.1                    py37_0  
pcre                      8.44                 he6710b0_0  
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pip                       20.3.3           py37h06a4308_0  
pixman                    0.40.0               h7b6447c_0  
plotly                    4.14.3             pyhd3eb1b0_0  
prometheus_client         0.9.0              pyhd3eb1b0_0  
prompt-toolkit            3.0.8                      py_0  
prompt_toolkit            3.0.8                         0  
ptyprocess                0.7.0              pyhd3eb1b0_2  
pycparser                 2.20                       py_2  
pygments                  2.7.4              pyhd3eb1b0_0  
pynndescent               0.5.2              pyh44b312d_0    conda-forge
pyopenssl                 21.0.0             pyhd3eb1b0_1  
pyparsing                 2.4.7              pyhd3eb1b0_0  
pyqt                      5.9.2            py37h05f1152_2  
pyrsistent                0.17.3           py37h7b6447c_0  
pysocks                   1.7.1                    py37_1  
pytables                  3.6.1            py37he17a9a8_3    conda-forge
python                    3.7.9                h7579374_0  
python-dateutil           2.8.1              pyhd3eb1b0_0  
python-slugify            4.0.1                      py_0  
python_abi                3.7                     1_cp37m    conda-forge
pytz                      2021.1             pyhd3eb1b0_0  
pyzmq                     20.0.0           py37h2531618_1  
qt                        5.9.7                h5867ecd_1  
qtconsole                 5.0.2              pyhd3eb1b0_0  
qtpy                      1.9.0                      py_0  
r-askpass                 1.0               r36h14c3975_0  
r-assertthat              0.2.1             r36h6115d3f_0  
r-backports               1.1.4             r36h96ca727_0  
r-base                    3.6.1                haffb61f_2  
r-base64enc               0.1_3             r36h96ca727_4  
r-bh                      1.69.0_1          r36h6115d3f_0  
r-bit                     1.1_14            r36h96ca727_0  
r-bit64                   0.9_7             r36h96ca727_0  
r-blob                    1.1.1             r36h6115d3f_0  
r-boot                    1.3_20            r36h6115d3f_0  
r-broom                   0.5.2             r36h6115d3f_0  
r-callr                   3.2.0             r36h6115d3f_0  
r-caret                   6.0_83            r36h96ca727_0  
r-cellranger              1.1.0             r36h6115d3f_0  
r-class                   7.3_15            r36h96ca727_0  
r-cli                     1.1.0             r36h6115d3f_0  
r-clipr                   0.6.0             r36h6115d3f_0  
r-clisymbols              1.2.0             r36h6115d3f_0  
r-cluster                 2.0.8             r36ha65eedd_0  
r-codetools               0.2_16            r36h6115d3f_0  
r-colorspace              1.4_1             r36h96ca727_0  
r-cowplot                 1.1.1             r36hc72bb7e_0    conda-forge
r-crayon                  1.3.4             r36h6115d3f_0  
r-curl                    3.3               r36h96ca727_0  
r-data.table              1.12.2            r36h96ca727_0  
r-dbi                     1.0.0             r36h6115d3f_0  
r-dbplyr                  1.4.0             r36h6115d3f_0  
r-desc                    1.2.0             r36h6115d3f_0  
r-devtools                2.0.2             r36h6115d3f_0  
r-dichromat               2.0_0             r36h6115d3f_4  
r-digest                  0.6.18            r36h96ca727_0  
r-distutils               1.0             r36h516909a_1003    conda-forge
r-dplyr                   0.8.0.1           r36h29659fb_0  
r-ellipsis                0.1.0             r36h96ca727_0  
r-elpigraph.r             1.0.0           r36h516909a_1003    conda-forge
r-essentials              3.6.0                     r36_0  
r-evaluate                0.13              r36h6115d3f_0  
r-fansi                   0.4.0             r36h96ca727_0  
r-farver                  1.1.0             r36h29659fb_0  
r-forcats                 0.4.0             r36h6115d3f_0  
r-foreach                 1.4.4             r36h6115d3f_0  
r-foreign                 0.8_71            r36h96ca727_0  
r-formatr                 1.6               r36h6115d3f_0  
r-fs                      1.2.7             r36h29659fb_0  
r-generics                0.0.2             r36h6115d3f_0  
r-gensa                   1.1.7             r36h29659fb_0  
r-ggforce                 0.3.2             r36h0357c0b_0    conda-forge
r-ggplot2                 3.1.1             r36h6115d3f_0  
r-ggpubr                  0.2.5             r36h6115d3f_1    conda-forge
r-ggrepel                 0.8.2             r36h0357c0b_1    conda-forge
r-ggsci                   2.9             r36h6115d3f_1003    conda-forge
r-ggsignif                0.6.0             r36h6115d3f_1    conda-forge
r-gh                      1.0.1             r36h6115d3f_0  
r-git2r                   0.25.2            r36h96ca727_0  
r-glmnet                  2.0_16            r36ha65eedd_0  
r-glue                    1.3.1             r36h96ca727_0  
r-gower                   0.2.0             r36h96ca727_0  
r-gridextra               2.3               r36h6115d3f_0  
r-gtable                  0.3.0             r36h6115d3f_0  
r-haven                   2.1.0             r36h29659fb_0  
r-hexbin                  1.27.2            r36ha65eedd_0  
r-highr                   0.8               r36h6115d3f_0  
r-hms                     0.4.2             r36h6115d3f_0  
r-htmltools               0.3.6             r36h29659fb_0  
r-htmlwidgets             1.3               r36h6115d3f_0  
r-httpuv                  1.5.1             r36h29659fb_0  
r-httr                    1.4.0             r36h6115d3f_0  
r-igraph                  1.2.4.1           r36h80f5a37_0  
r-infotheo                1.2.0             r36h29659fb_0  
r-ini                     0.3.1             r36h6115d3f_0  
r-ipred                   0.9_8             r36h96ca727_0  
r-irdisplay               0.7.0             r36h6115d3f_0  
r-irkernel                0.8.15                    r36_0  
r-irlba                   2.3.3             r36h96ca727_0  
r-iterators               1.0.10            r36h6115d3f_0  
r-jsonlite                1.6               r36h96ca727_0  
r-kernsmooth              2.23_15           r36ha65eedd_4  
r-knitr                   1.22              r36h6115d3f_0  
r-labeling                0.3               r36h6115d3f_4  
r-later                   0.8.0             r36h29659fb_0  
r-lattice                 0.20_38           r36h96ca727_0  
r-lava                    1.6.5             r36h6115d3f_0  
r-lazyeval                0.2.2             r36h96ca727_0  
r-lubridate               1.7.4             r36h29659fb_0  
r-magrittr                1.5               r36h6115d3f_4  
r-maps                    3.3.0             r36h96ca727_0  
r-markdown                0.9               r36h96ca727_0  
r-mass                    7.3_51.3          r36h96ca727_0  
r-matrix                  1.2_17            r36h96ca727_0  
r-memoise                 1.1.0             r36h6115d3f_0  
r-mgcv                    1.8_28            r36h96ca727_0  
r-mime                    0.6               r36h96ca727_0  
r-modelmetrics            1.2.2             r36h29659fb_0  
r-modelr                  0.1.4             r36h6115d3f_0  
r-munsell                 0.5.0             r36h6115d3f_0  
r-nlme                    3.1_139           r36ha65eedd_0  
r-nnet                    7.3_12            r36h96ca727_0  
r-numderiv                2016.8_1          r36h6115d3f_0  
r-openssl                 1.3               r36h96ca727_0  
r-pbdzmq                  0.3_3             r36h5455479_1  
r-pillar                  1.3.1             r36h6115d3f_0  
r-pkgbuild                1.0.3             r36h6115d3f_0  
r-pkgconfig               2.0.2             r36h6115d3f_0  
r-pkgload                 1.0.2             r36h29659fb_0  
r-plogr                   0.2.0             r36h6115d3f_0  
r-plyr                    1.8.4             r36h29659fb_0  
r-polyclip                1.10_0            r36h29659fb_0  
r-polynom                 1.4_0             r36h6115d3f_0  
r-prettyunits             1.0.2             r36h6115d3f_0  
r-processx                3.3.0             r36h96ca727_0  
r-prodlim                 2018.04.18        r36h29659fb_0  
r-progress                1.2.0             r36h6115d3f_0  
r-promises                1.0.1             r36h29659fb_0  
r-ps                      1.3.0             r36h96ca727_0  
r-purrr                   0.3.2             r36h96ca727_0  
r-quantmod                0.4_14            r36h6115d3f_0  
r-r6                      2.4.0             r36h6115d3f_0  
r-randomforest            4.6_14            r36ha65eedd_0  
r-rbokeh                  0.6.3                     r36_0  
r-rcmdcheck               1.3.2             r36h6115d3f_0  
r-rcolorbrewer            1.1_2             r36h6115d3f_0  
r-rcpp                    1.0.1             r36h29659fb_0  
r-rcpparmadillo           0.9.300.2.0       r36h29659fb_0  
r-rcppeigen               0.3.3.5.0         r36h29659fb_0  
r-rcpproll                0.3.0             r36h29659fb_0  
r-readr                   1.3.1             r36h29659fb_0  
r-readxl                  1.3.1             r36h29659fb_0  
r-recipes                 0.1.5             r36h6115d3f_0  
r-recommended             3.6.0                     r36_0  
r-rematch                 1.0.1             r36h6115d3f_0  
r-remotes                 2.0.4             r36h6115d3f_0  
r-repr                    0.19.2            r36h6115d3f_0  
r-reprex                  0.2.1             r36h6115d3f_0  
r-reshape2                1.4.3             r36h29659fb_0  
r-rlang                   0.3.4             r36h96ca727_0  
r-rmarkdown               1.12              r36h6115d3f_0  
r-rpart                   4.1_15            r36h96ca727_0  
r-rprojroot               1.3_2             r36h6115d3f_0  
r-rsqlite                 2.1.1             r36h29659fb_0  
r-rstudioapi              0.10              r36h6115d3f_0  
r-rvest                   0.3.3             r36h6115d3f_0  
r-scales                  1.0.0             r36h29659fb_0  
r-segmented               1.0_0             r36h6115d3f_0  
r-selectr                 0.4_1             r36h6115d3f_0  
r-sessioninfo             1.1.1             r36h6115d3f_0  
r-shiny                   1.3.2             r36h6115d3f_0  
r-sourcetools             0.1.7             r36h29659fb_0  
r-spatial                 7.3_11            r36h96ca727_4  
r-squarem                 2017.10_1         r36h6115d3f_0  
r-stringi                 1.4.3             r36h29659fb_0  
r-stringr                 1.4.0             r36h6115d3f_0  
r-survival                2.44_1.1          r36h96ca727_0  
r-sys                     3.2               r36h96ca727_0  
r-tibble                  2.1.1             r36h96ca727_0  
r-tictoc                  1.0               r36h6115d3f_0  
r-tidyr                   0.8.3             r36h29659fb_0  
r-tidyselect              0.2.5             r36h29659fb_0  
r-tidyverse               1.2.1             r36h6115d3f_0  
r-timedate                3043.102          r36h6115d3f_0  
r-tinytex                 0.12              r36h6115d3f_0  
r-ttr                     0.23_4            r36ha65eedd_0  
r-tweenr                  1.0.1           r36h0357c0b_1002    conda-forge
r-usethis                 1.5.0             r36h6115d3f_0  
r-utf8                    1.1.4             r36h96ca727_0  
r-uuid                    0.1_2             r36h96ca727_4  
r-vgam                    1.1_1             r36ha65eedd_0  
r-viridislite             0.3.0             r36h6115d3f_0  
r-whisker                 0.3_2             r36h6115d3f_4  
r-withr                   2.1.2             r36h6115d3f_0  
r-xfun                    0.6               r36h6115d3f_0  
r-xml                     3.98_1.19         r36h96ca727_0  
r-xml2                    1.2.0             r36h29659fb_0  
r-xopen                   1.0.0             r36h6115d3f_0  
r-xtable                  1.8_4             r36h6115d3f_0  
r-xts                     0.11_2            r36h96ca727_0  
r-yaml                    2.2.0             r36h96ca727_0  
r-zoo                     1.8_6             r36h96ca727_0  
readline                  8.1                  h27cfd23_0  
requests                  2.27.1             pyhd3eb1b0_0  
retrying                  1.3.3                      py_2  
rpy2                      2.9.4           py37r36hd767a1f_3    conda-forge
scanpy                    1.6.0                      py_0    bioconda
scikit-learn              0.23.2           py37h0573a6f_0  
scipy                     1.6.0            py37h91f5cce_0  
seaborn                   0.11.1             pyhd3eb1b0_0  
send2trash                1.5.0              pyhd3eb1b0_1  
setuptools                52.0.0           py37h06a4308_0  
setuptools-scm            6.3.2              pyhd3eb1b0_0  
setuptools_scm            6.3.2                hd3eb1b0_0  
shapely                   1.7.1            py37h98ec03d_0  
simplegeneric             0.8.1                    py37_2  
sinfo                     0.3.1                      py_0    conda-forge
sip                       4.19.8           py37hf484d3e_0  
six                       1.15.0             pyhd3eb1b0_0  
snowballstemmer           2.2.0              pyhd3eb1b0_0  
sphinx                    4.2.0              pyhd3eb1b0_1  
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0  
sqlite                    3.33.0               h62c20be_0  
statsmodels               0.12.1           py37h27cfd23_0  
stdlib-list               0.7.0                      py_2    conda-forge
stream                    1.0                        py_0    bioconda
tbb                       2020.3               hfd86e86_0  
terminado                 0.9.2            py37h06a4308_0  
testpath                  0.4.4              pyhd3eb1b0_0  
text-unidecode            1.3                        py_0  
threadpoolctl             2.1.0              pyh5ca1d4c_0  
tk                        8.6.10               hbc83047_0  
tktable                   2.10                 h14c3975_0  
tomli                     1.2.2              pyhd3eb1b0_0  
tornado                   6.1              py37h27cfd23_0  
tqdm                      4.62.3             pyhd3eb1b0_1  
traitlets                 5.0.5              pyhd3eb1b0_0  
tzlocal                   2.1                      py37_0  
umap-learn                0.5.1            py37h89c1867_0    conda-forge
unidecode                 1.1.2              pyhd3eb1b0_0  
unzip                     6.0                  h611a1e1_0  
urllib3                   1.26.7             pyhd3eb1b0_0  
wcwidth                   0.2.5                      py_0  
webencodings              0.5.1                    py37_1  
wheel                     0.36.2             pyhd3eb1b0_0  
widgetsnbextension        3.5.1                    py37_0  
xz                        5.2.5                h7b6447c_0  
zeromq                    4.3.3                he6710b0_3  
zip                       3.0                  h1adfe0e_0  
zipp                      3.4.0              pyhd3eb1b0_0  
zlib                      1.2.11               h7b6447c_3  
zstd                      1.4.5                h9ceee32_0  

What are your suggestions ?
Thanks for the help,
Best
Lea