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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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cannot pickle 'weakref.ReferenceType' object
#336
mousepixels
closed
7 months ago
1
Determine which version of cellbender was used for a run
#335
chris-rands
opened
7 months ago
0
Negative raw counts
#334
IrinaVKuznetsova
closed
7 months ago
0
seeking guidance for the rank to set for empty droplets
#333
Domoun
opened
7 months ago
0
CellBender can not remove the backgroud very well using the output of STARsolo
#332
JianhuaWang95
opened
7 months ago
0
IndexError: index 9500 is out of bounds for axis 0 with size 9500**
#331
imrankhan27
opened
7 months ago
0
different priors on GPU vs. CPU?
#330
bobermayer
opened
7 months ago
0
Crash after completing "Working on chunk (xx / xx)"
#329
Thapeachydude
opened
7 months ago
4
No space left on device
#328
IrinaVKuznetsova
opened
8 months ago
1
Error generating HTML report?
#327
razorofockham
opened
8 months ago
2
Barcode Multiplets
#326
PurwinTJ
opened
8 months ago
0
Intepreting nuclei cellbender output
#325
marcus-tutert
opened
8 months ago
0
missing tab/release in GitHub + release on PyPI for v0.3.1
#324
boegel
opened
8 months ago
2
ValueError: cannot infer dimensions from zero sized index arrays
#323
OneHitKO
opened
8 months ago
6
Cell Bender output pdf file
#322
Seoyeon-Y
opened
8 months ago
0
Query: Using CellBender on Multiple scRNA-seq Samples
#321
ryan2han
closed
8 months ago
2
the remove-background data named output.h5 has 0 genes.
#320
Tycooner
opened
9 months ago
4
the remove-background data named output.h5 has 0 genes. why?
#319
Tycooner
closed
9 months ago
0
the output.h5 has 0 genes ? it is so strange!
#318
Tycooner
closed
9 months ago
0
Test ELBO higher than train ELBO
#317
ellimarip
opened
9 months ago
1
extracting counts data from cellbender/seurat h5
#316
bsmith030465
opened
9 months ago
0
Cellbender v.0.3.0 not working with Seurat Read10X_h5 function
#315
smk5g5
opened
9 months ago
3
h5ad input
#314
SEVEN-XYCHEN
opened
9 months ago
0
Input file
#313
SEVEN-XYCHEN
opened
9 months ago
0
Don't crash with ZeroDivisionError if initial test ELBO is the best test ELBO
#312
alecw
closed
5 months ago
3
Cellbender paper - UMAPs
#311
dbuszta
opened
10 months ago
0
Mitochondrial genes are not removed for NucSeq in v0.3
#310
schmeing
opened
10 months ago
1
Different python version
#309
malonzm1
opened
10 months ago
0
No counts matrix in my AnnData object after importing the out h5 file
#308
b-neumann
opened
10 months ago
0
Selecting specific GPU in multi-GPU environment
#307
Nico995
opened
10 months ago
1
negative entries in filtered count matrix?
#306
bobermayer
opened
10 months ago
7
Additional diagnostic plots
#305
wmacnair
opened
11 months ago
0
Bump version
#304
sjfleming
closed
11 months ago
0
v0.3.1
#303
sjfleming
closed
11 months ago
0
Fix bugs with report generation across platforms
#302
sjfleming
closed
11 months ago
0
Docker image: Could not save checkpoint (python3.7), due to [enforce fail at inline_container.cc:445] . PytorchStreamWriter failed
#301
plijnzaad
opened
11 months ago
2
errors writing html file
#300
MengjunWu
opened
11 months ago
3
Working with the 'posterior' output - per documentation.
#299
benemead
opened
11 months ago
9
RuntimeError: CUDA error: CUBLAS_STATUS_INVALID_VALUE when calling `cublasSgemm
#298
alexcwsmith
opened
11 months ago
2
Using CellBender on sc/sn-RNA-seq and CITE-seq samples part of multi-sample cohort setting
#297
browaeysrobin
opened
11 months ago
1
TypeError: cannot pickle 'weakref.ReferenceType' object
#296
lili03080317
opened
11 months ago
13
CUDA out of memory at MCKP estimator step
#295
Terkild
opened
1 year ago
4
"Final test ELBO is much lower than the max test ELBO." in a seemingly correct result.
#294
ZhangMH2000
opened
1 year ago
3
ValueError: cannot convert float NaN to integer
#293
sjfleming
opened
1 year ago
0
warning: different learning-rate trying and gene decreased dramatically after cellbender removal
#292
GLLMU
opened
1 year ago
2
Significance of differences in PCA plot and average_counts_removed_per_cell metric with different settings
#291
RvdKwast
opened
1 year ago
1
save checkpoint to a designated directory?
#290
LiQian-XC
opened
1 year ago
5
cellbender on Crispr guide capture?
#289
kawairine
opened
1 year ago
0
Can CellBender help improve demultiplexing of multiplexed samples?
#288
RvdKwast
opened
1 year ago
0
Windows no output PDF no output HTML report
#287
sjfleming
opened
1 year ago
1
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