broadinstitute/CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
PythonBSD-3-Clause
Pinned issues
Issues
- 3
- 5
- 7
Not saving ckpt.tar.gz checkpoint
#371 opened by IsauraMaria96 - 6
HTML output fails due to lxml change
#348 opened by sjfleming - 2
Background Fraction
#369 opened by hk2rma - 0
- 1
- 8
- 0
CellBender for .BAM file
#375 opened by jzheng25 - 0
RuntimeError: CUDA driver error: invalid argument - Google Container Registry (GCR)
#374 opened by AClab-sgarcia - 0
Cellbender on multiplexed chemistries
#373 opened by LinearParadox - 1
Fixed Single cell RNA seq
#372 opened by archana433 - 0
OOM posterior inference for chimeric sample even using --posterior-batch-size 1
#370 opened by njbernstein - 1
New fileformat output from BD rhapsody
#359 opened by MelanieRN - 0
Importance of model loss
#366 opened by ShadHOH - 2
Error generating HTML report?
#327 opened by razorofockham - 1
- 3
- 2
Index Error in priors.py
#343 opened by Ratoncito - 0
Never mind
#364 opened by maxwellfinkelstein - 0
Unhandled division by zero
#363 opened by fm361 - 0
Computing the output in asynchronous chunks in parallel takes longer than 144 hours
#362 opened by Erhei130 - 1
Question about input h5 file
#361 opened by Linxiaobuskiy - 0
Should I keep decreasing the learning rate?
#360 opened by txemaheredia - 0
Number of cells after cellbender much more than number of cells from cellranger (filtered)
#358 opened by pc2001 - 0
"Trying to use CUDA, " \ AssertionError: Trying to use CUDA, but CUDA is not available.
#357 opened by shnsk1995 - 0
- 1
ERROR: Could not build wheels for pyzmq, which is required to install pyproject.toml-based projects
#344 opened by axiba053 - 0
cellbender v3.0 doesn't generate most of the output files, but doesn't have any errors
#356 opened by cswoboda - 0
How to run CellBender for a pooling library?
#354 opened by tewengtong - 0
Is it possible to adjust the priors so that cellbender can work with shallow-sequenced data?
#353 opened by onurcanbektas - 2
Problem installing cellbender
#351 opened by marctormo - 1
- 1
How to deal with "The expression of the highly-expressed gene _ decreases quite markedly after CellBender. Check to ensure this makes sense!" warning?
#342 opened by Ratoncito - 1
Fix readthedocs
#346 opened by sjfleming - 1
Feature: tool for users to rescue v0.3.1 runs and to re-compute output counts in general
#349 opened by sjfleming - 2
- 0
Problems interpreting results
#338 opened by MarP2606 - 1
cannot pickle 'weakref.ReferenceType' object
#336 opened by mousepixels - 0
- 0
Negative raw counts
#334 opened by IrinaVKuznetsova - 0
- 0
CellBender can not remove the backgroud very well using the output of STARsolo
#332 opened by JianhuaWang95 - 0
- 0
different priors on GPU vs. CPU?
#330 opened by bobermayer - 1
No space left on device
#328 opened by IrinaVKuznetsova - 0
Barcode Multiplets
#326 opened by PurwinTJ - 0
Intepreting nuclei cellbender output
#325 opened by GelatinousGiant - 2
- 0
Cell Bender output pdf file
#322 opened by Seoyeon-Y