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broadinstitute
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CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
https://cellbender.rtfd.io
BSD 3-Clause "New" or "Revised" License
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Error handling MTX format inputs in WDL
#245
sjfleming
closed
7 months ago
0
missing features?
#244
kunalkathuria
closed
1 year ago
6
Working with CellBender outputs in R
#243
sjfleming
closed
1 year ago
0
Demo run using Google Colab GPU for free
#242
sjfleming
closed
1 year ago
1
FileNotFoundError: [Errno 2] No such file or directory: 'ckpt.tar.gz.tmp' -> 'ckpt.tar.gz'
#241
pengxin2019
opened
1 year ago
12
Move from setup.py to pyproject.toml
#240
sjfleming
closed
1 year ago
0
Error uploading package to PyPI
#239
sjfleming
closed
7 months ago
1
v0.3.0
#238
sjfleming
closed
1 year ago
0
Giant squashed commit
#237
sjfleming
closed
1 year ago
0
Fix issues with encoder and several bug fixes
#236
sjfleming
closed
1 year ago
0
Save intermediate checkpoints using a separate process
#235
sjfleming
opened
1 year ago
0
Cellbender output contains deprecated probes and probes with off target activity
#234
martina-morchio
opened
1 year ago
15
Enable setting the count prior for empty droplets
#233
niklasmueboe
closed
1 year ago
2
How can I make UMAPs with and without(on the same set of cell barcodes)
#232
ruiqiizhou
opened
1 year ago
1
ELBO drop for training but not for test set
#231
xinyixinyijiang
closed
1 year ago
2
Cannot save checkpoint file
#230
racng
closed
1 year ago
10
Unsure how to interpret cell probabilities
#229
egatlas
opened
1 year ago
2
Cellbender unable to detect CUDA version 12
#228
unikill066
opened
1 year ago
2
error running scanpy highly_variable_genes
#227
kunalkathuria
opened
1 year ago
2
SPLiTseq
#226
ybaeus
opened
1 year ago
10
index 14365 is out of bounds for axis 0 with size 14365
#225
nouhaylaeraysy
closed
1 year ago
10
Try L4 gpu as default for WDL
#224
sjfleming
opened
1 year ago
0
No cells found when excluding the ADT
#223
aodainic7
opened
1 year ago
6
Request foe help with cellbender graph
#222
beetlejuice007
closed
1 year ago
2
issue running train.py AttributeError: module 'pyro.optim' has no attribute 'OneCycleLR'
#221
rLannes
closed
1 year ago
2
Cell probabilities remain close to one
#220
leprohonmalo
closed
1 year ago
9
Converged inference but uncertain cell probabilities
#219
mariecrane
closed
1 year ago
2
Github action to test pip install from branch
#218
sjfleming
closed
1 year ago
0
Error while trying to load cellbender filtered output to scanpy
#217
unikill066
closed
1 year ago
3
change http client library
#216
dogTK
closed
1 year ago
2
change http clinet library
#215
dogTK
closed
1 year ago
0
Cannot download sample of dataset
#214
dogTK
closed
1 year ago
4
fix example datasets_url
#213
dogTK
closed
1 year ago
2
Can't pickle `weakref` objects when saving checkpoints
#212
tzeitim
opened
1 year ago
3
Understanding cellbender plots
#211
smk5g5
closed
1 year ago
13
Meaning of count removal per gene warning (v0.3.0)
#210
npklein
opened
1 year ago
3
Trouble installing dev branch
#209
ollieeknight
closed
1 year ago
9
Write posterior as h5, and some estimator improvements
#208
sjfleming
closed
1 year ago
1
argmax error in estimation.py
#207
HJ234
closed
1 year ago
6
Examine Mean estimator for speedups
#206
sjfleming
opened
1 year ago
1
Save posterior as h5 rather than npz
#205
sjfleming
closed
1 year ago
1
Duplicated var_names in cellbender output
#204
auesro
closed
1 year ago
3
Move project to python 3.8
#203
sjfleming
opened
1 year ago
4
Add soft constraints to the model for semi-supervision of cell probabilities
#202
sjfleming
closed
1 year ago
1
Add multiprocessing option for the MCKP estimator
#201
sjfleming
closed
1 year ago
0
Truncated Cell Barcodes
#200
ayyildizd
closed
1 year ago
5
Training & test curves are strange shape
#199
twoneu
closed
1 year ago
2
Degeneracy between d_cell and epsilon
#198
sjfleming
closed
1 year ago
1
No empty droplets detected
#197
hviolaphd
opened
1 year ago
2
Address MCKP memory issues
#196
sjfleming
closed
1 year ago
2
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