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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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The raw counts calculated by cellbender is different from the raw counts of input file
#286
YiweiNiu
closed
1 year ago
2
cellbender v0.3.0 failed to remove ambient RNA contamination, what should I do?
#285
YiweiNiu
closed
1 year ago
2
Compatibility with 10X Multiome data?
#284
AndiL04
opened
1 year ago
5
CellBender Remove-Background: Exploring Hyperparameter Effects
#283
unikill066
opened
1 year ago
2
generate tiny dataset syntax error
#282
ryao-mdanderson
opened
1 year ago
3
cellbender v0.3 h5 output works with BPCells
#281
mihem
opened
1 year ago
1
gpu enabled cellbender container
#280
ryao-mdanderson
opened
1 year ago
4
Feature request: more comparisons with 10x outputs
#279
cyrilcros
opened
1 year ago
4
Unable to create HTML report (Cellbender version 0.3.0)
#278
TeodoraTockovska
opened
1 year ago
7
How can i downgrade to CellBender 0.2?
#277
amini-sahand
opened
1 year ago
5
Reducing the learning rate and unexpected number of cells
#276
mihem
closed
1 year ago
10
Could not save checkpoint/cannot pickle 'weakref' object
#275
ndrubins
closed
1 year ago
1
Feat: Using output from Kallisto/Bustools (or other non-CellRanger pipelines)
#274
yfarjoun
closed
1 year ago
3
Failed to generate HTML report: `UnicodeDecodeError: 'ascii' codec can't decode byte`
#273
asherkhb-ktx
opened
1 year ago
10
Suitable for microwell platform?
#272
Li-ZhiD
opened
1 year ago
2
Impact of using different cellbender parameters across samples on downstream analysis
#271
dquintanatorres
opened
1 year ago
1
different performance between 0.2.0 and 0.3.0
#270
huananfshi
closed
1 year ago
8
Running Cellbender with multiple fpr
#269
cyrilcros
opened
1 year ago
1
There is an entry in the output greater than the input
#268
jg9zk
closed
1 year ago
9
multiple parallel run - checkpoint file
#267
muntajihad
opened
1 year ago
5
reuse of checkpoint file
#266
qianzhengzong
opened
1 year ago
6
Problem generating report
#265
ps2504
opened
1 year ago
3
MCKP gene iterator speedup
#264
sjfleming
closed
1 year ago
0
Memory-efficient posterior generation
#263
sjfleming
closed
11 months ago
6
Difference in array size of 'features_analyzed_inds' and 'ambient_expression'
#262
racng
closed
1 year ago
2
DGE loader can be more memory efficient
#261
sjfleming
opened
1 year ago
0
os.replace() instead of os.rename() to save checkpoint
#260
sjfleming
closed
1 year ago
0
Fix posterior and estimator integer overflow bugs on Windows
#259
sjfleming
closed
11 months ago
7
Move hash computation so that it is recomputed on retry, and now-inva…
#258
alecw
closed
11 months ago
2
Create a multiqc module
#257
grst
opened
1 year ago
3
Help with reducing number of cells called
#256
racng
opened
1 year ago
7
Fewer than 4 cells passed to encoder minibatch
#255
fansalon
closed
1 year ago
3
Run on Parse Biosciences output
#254
thisisamirv
closed
1 year ago
2
os.replace() instead of os.rename() to save checkpoint
#253
sjfleming
closed
1 year ago
1
Posterior computation ValueError: 'shape' elements cannot be negative
#252
sjfleming
closed
6 months ago
15
OOM Killed during batch processing when running cellbender on slurm
#251
ggconnell
opened
1 year ago
8
FileExistsError: [WinError 183] Cannot create a file when that file already exists: 'ckpt.tar.gz.tmp' -> 'ckpt.tar.gz'
#250
jamesjcai
closed
1 year ago
7
Fix typos in h5 explanation in docs
#249
sjfleming
opened
1 year ago
0
Minimize memory usage during posterior generation
#248
sjfleming
opened
1 year ago
1
Add WDL input to set number of retries.
#247
kshakir
closed
11 months ago
1
Bug fix for WDL using MTX input
#246
sjfleming
closed
11 months ago
0
Error handling MTX format inputs in WDL
#245
sjfleming
closed
6 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
11 months ago
0
Error uploading package to PyPI
#239
sjfleming
closed
6 months ago
1
v0.3.0
#238
sjfleming
closed
1 year ago
0
Giant squashed commit
#237
sjfleming
closed
1 year ago
0
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