broadinstitute CellBender issues

broadinstitute / 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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issues

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OOM posterior inference for chimeric sample even using --posterior-batch-size 1

#370 njbernstein opened 1 day ago
0
Background Fraction

#369 hk2rma opened 5 days ago
0
v0.3.2

#368 sjfleming closed 1 week ago
0
Azurize CellBender to run on ToA

#367 aawdeh closed 1 week ago
5
Importance of model loss

#366 ShadHOH opened 2 weeks ago
0
Can't Computing target noise counts per gene for MCKP estimator

#365 Deroline10 opened 3 weeks ago
1
Never mind

#364 maxwellfinkelstein closed 3 weeks ago
0
Unhandled division by zero

#363 fm361 opened 1 month ago
0
Computing the output in asynchronous chunks in parallel takes longer than 144 hours

#362 Erhei130 opened 1 month ago
0
Question about input h5 file

#361 Linxiaobuskiy opened 1 month ago
1
Should I keep decreasing the learning rate?

#360 txemaheredia opened 1 month ago
0
New fileformat output from BD rhapsody

#359 MelanieRN opened 1 month ago
1
Number of cells after cellbender much more than number of cells from cellranger (filtered)

#358 pc2001 opened 1 month ago
0
"Trying to use CUDA, " \ AssertionError: Trying to use CUDA, but CUDA is not available.

#357 shnsk1995 opened 1 month ago
0
cellbender v3.0 doesn't generate most of the output files, but doesn't have any errors

#356 cswoboda opened 1 month ago
0
Numpy build failed when installing cell bender from source

#355 shnsk1995 closed 1 month ago
0
How to run CellBender for a pooling library?

#354 tewengtong opened 1 month ago
0
Is it possible to adjust the priors so that cellbender can work with shallow-sequenced data?

#353 onurcanbektas opened 2 months ago
0
Readme appearance

#352 sjfleming closed 2 months ago
0
Problem installing cellbender

#351 marctormo opened 2 months ago
2
Fix v0.3.1 bug

#350 sjfleming closed 2 months ago
0
Feature: tool for users to rescue v0.3.1 runs and to re-compute output counts in general

#349 sjfleming closed 2 months ago
1
HTML output fails due to lxml change

#348 sjfleming closed 2 months ago
5
Fix major bug in v0.3.1: negative counts

#347 sjfleming closed 2 months ago
3
Fix readthedocs

#346 sjfleming closed 2 months ago
1
Fix exception loading checkpoint

#345 alecw closed 2 months ago
3
ERROR: Could not build wheels for pyzmq, which is required to install pyproject.toml-based projects

#344 axiba053 opened 3 months ago
1
Index Error in priors.py

#343 Ratoncito opened 3 months ago
2
How to deal with "The expression of the highly-expressed gene _ decreases quite markedly after CellBender. Check to ensure this makes sense!" warning?

#342 Ratoncito opened 3 months ago
1
Changed np.int to np.int64 as the use of np.int is now deprecated

#341 GreenGilad closed 2 months ago
1
Cell Ranger 'Multiplexing Capture' feature type not recognised.

#340 jpintar opened 3 months ago
1
Update cli.py to add newer Cell Ranger feature types

#339 jpintar closed 2 months ago
1
Problems interpreting results

#338 MarP2606 opened 3 months ago
0
CellBender ran successfully but no HTML report generated

#337 wendy0853 opened 4 months ago
7
cannot pickle 'weakref.ReferenceType' object

#336 mousepixels closed 4 months ago
1
Determine which version of cellbender was used for a run

#335 chris-rands opened 4 months ago
0
Negative raw counts

#334 IrinaVKuznetsova closed 4 months ago
0
seeking guidance for the rank to set for empty droplets

#333 Domoun opened 4 months ago
0
CellBender can not remove the backgroud very well using the output of STARsolo

#332 JianhuaWang95 opened 4 months ago
0
IndexError: index 9500 is out of bounds for axis 0 with size 9500**

#331 imrankhan27 opened 4 months ago
0
different priors on GPU vs. CPU?

#330 bobermayer opened 4 months ago
0
Crash after completing "Working on chunk (xx / xx)"

#329 Thapeachydude opened 4 months ago
3
No space left on device

#328 IrinaVKuznetsova opened 4 months ago
1
Error generating HTML report?

#327 razorofockham opened 5 months ago
2
Barcode Multiplets

#326 PurwinTJ opened 5 months ago
0
Intepreting nuclei cellbender output

#325 GelatinousGiant opened 5 months ago
0
missing tab/release in GitHub + release on PyPI for v0.3.1

#324 boegel opened 5 months ago
2
ValueError: cannot infer dimensions from zero sized index arrays

#323 OneHitKO closed 2 weeks ago
4
Cell Bender output pdf file

#322 Seoyeon-Y opened 5 months ago
0
Query: Using CellBender on Multiple scRNA-seq Samples

#321 ryan2han closed 5 months ago
2