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

298 stars 54 forks source link

issues

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Save checkpoint fails

#395 christophista closed 6 days ago
1
CXXABI_1.3.9

#394 robin-sto opened 1 week ago
0
WISH: Please respect CGroups CPU limits for parallelization, or default to single-core processing

#393 HenrikBengtsson opened 1 week ago
0
fixed tarball wrong save name

#392 ianfd opened 3 weeks ago
0
use `args.total_droplets` to instantiate dataset

#391 colobas opened 1 month ago
0
Inappropriate hard-coded constant `const.MAX_TOTAL_DROPLETS_GUESSED` for large datasets?

#390 colobas opened 1 month ago
0
Unexpected Increases in nCount and nFeature Post-CellBender Processing

#389 echovv opened 1 month ago
0
simpleaf + cellbender does not seem to function well

#388 robertzeibich opened 1 month ago
0
Docker container: "Trying to use CUDA, but CUDA is not available."

#387 onurcanbektas closed 1 month ago
0
Report issue saving checkpoint

#386 acerdenno opened 1 month ago
4
cannot find examples/remove_background/generate_tiny_10x_dataset.py

#385 Rfriedmancolumbia closed 2 months ago
0
Report output fails when count matrix has float counts instead of integers

#384 MNM-TB opened 2 months ago
0
webcolors version problem

#383 nictru opened 2 months ago
0
struct.error: 'i' format requires -2147483648 <= number <= 2147483647

#382 yuanjianwen-gif opened 2 months ago
0
Coupling CellBender w/ other preprocessing tools--doublet detection, demultiplexing

#381 lhoranportelance opened 2 months ago
1
load_anndata_from_input_and_output: retain_input_metadata input to nowhere

#380 benemead opened 3 months ago
2
NM

#379 ghost opened 3 months ago
0
raw h5ad OR filtered h5ad

#378 elegantmedstu opened 3 months ago
1
Mismatch between summary for algorithm convergence and learning curve

#377 KaczorowskiLab opened 3 months ago
0
Increased number of UMIs per barcode after running remove-background

#376 hhvu0102 closed 3 months ago
1
CellBender for .BAM file

#375 jzheng25 opened 4 months ago
0
RuntimeError: CUDA driver error: invalid argument - Google Container Registry (GCR)

#374 AClab-sgarcia opened 4 months ago
0
Cellbender on multiplexed chemistries

#373 LinearParadox opened 4 months ago
1
Fixed Single cell RNA seq

#372 archana433 opened 4 months ago
1
Not saving ckpt.tar.gz checkpoint

#371 IsauraMaria96 opened 4 months ago
8
OOM posterior inference for chimeric sample even using --posterior-batch-size 1

#370 njbernstein opened 4 months ago
0
Background Fraction

#369 hk2rma opened 5 months ago
3
v0.3.2

#368 sjfleming closed 5 months ago
0
Azurize CellBender to run on ToA

#367 aawdeh closed 5 months ago
5
Importance of model loss

#366 ShadHOH opened 5 months ago
0
Can't Computing target noise counts per gene for MCKP estimator

#365 Deroline10 opened 5 months ago
1
Never mind

#364 maxwellfinkelstein closed 5 months ago
0
Unhandled division by zero

#363 fm361 opened 5 months ago
1
Computing the output in asynchronous chunks in parallel takes longer than 144 hours

#362 Erhei130 opened 6 months ago
1
Question about input h5 file

#361 Linxiaobuskiy opened 6 months ago
1
Should I keep decreasing the learning rate?

#360 txemaheredia opened 6 months ago
1
New fileformat output from BD rhapsody

#359 MelanieRN opened 6 months ago
1
Number of cells after cellbender much more than number of cells from cellranger (filtered)

#358 pc2001 opened 6 months ago
0
"Trying to use CUDA, " \ AssertionError: Trying to use CUDA, but CUDA is not available.

#357 shnsk1995 opened 6 months ago
0
cellbender v3.0 doesn't generate most of the output files, but doesn't have any errors

#356 cswoboda opened 6 months ago
1
Numpy build failed when installing cell bender from source

#355 shnsk1995 closed 6 months ago
0
How to run CellBender for a pooling library?

#354 tewengtong opened 6 months ago
0
Is it possible to adjust the priors so that cellbender can work with shallow-sequenced data?

#353 onurcanbektas opened 7 months ago
0
Readme appearance

#352 sjfleming closed 7 months ago
0
Problem installing cellbender

#351 marctormo opened 7 months ago
2
Fix v0.3.1 bug

#350 sjfleming closed 7 months ago
0
Feature: tool for users to rescue v0.3.1 runs and to re-compute output counts in general

#349 sjfleming closed 7 months ago
1
HTML output fails due to lxml change

#348 sjfleming closed 7 months ago
8
Fix major bug in v0.3.1: negative counts

#347 sjfleming closed 7 months ago
3
Fix readthedocs

#346 sjfleming closed 7 months ago
1