broadinstitute/CellBender

Issues

• Run cellbender after Cellranger aggr

  #398 opened 25 days ago by SimonE1220
  0

• Report issue saving checkpoint

  #386 opened 3 months ago by acerdenno
  5

• python 3.7 and torch < 0.2.0

  #397 opened a month ago by plijnzaad
  0

• Not saving ckpt.tar.gz checkpoint

  #371 opened 6 months ago by IsauraMaria96
  9

• OutOfMemory error when computing target noise counts per gene

  #396 opened a month ago by MattChristmas
  0

• Coupling CellBender w/ other preprocessing tools--doublet detection, demultiplexing

  #381 opened 4 months ago by lhoranportelance
  2

• Unhandled division by zero

  #363 opened 7 months ago by fm361
  1

• Save checkpoint fails

  #395 opened a month ago by christophista
  1

• Cellbender on multiplexed chemistries

  #373 opened 6 months ago by LinearParadox
  1

• CXXABI_1.3.9

  #394 opened a month ago by robin-sto
  0

• WISH: Please respect CGroups CPU limits for parallelization, or default to single-core processing

  #393 opened a month ago by HenrikBengtsson
  0

• HTML output fails due to lxml change

  #348 opened 9 months ago by sjfleming
  8

• cellbender v3.0 doesn't generate most of the output files, but doesn't have any errors

  #356 opened 8 months ago by cswoboda
  1

• Inappropriate hard-coded constant `const.MAX_TOTAL_DROPLETS_GUESSED` for large datasets?

  #390 opened 2 months ago by colobas
  0

• Unexpected Increases in nCount and nFeature Post-CellBender Processing

  #389 opened 2 months ago by echovv
  0

• Should I keep decreasing the learning rate?

  #360 opened 7 months ago by txemaheredia
  1

• simpleaf + cellbender does not seem to function well

  #388 opened 2 months ago by robertzeibich
  0

• Docker container: "Trying to use CUDA, but CUDA is not available."

  #387 opened 3 months ago by onurcanbektas
  0

• cannot find examples/remove_background/generate_tiny_10x_dataset.py

  #385 opened 3 months ago by Rfriedmancolumbia
  0

• Background Fraction

  #369 opened 6 months ago by hk2rma
  3

• NM

  #379 opened 4 months ago by EEKLUES
  0

• Report output fails when count matrix has float counts instead of integers

  #384 opened 4 months ago by MNM-TB
  0

• webcolors version problem

  #383 opened 4 months ago by nictru
  0

• struct.error: 'i' format requires -2147483648 <= number <= 2147483647

  #382 opened 4 months ago by yuanjianwen-gif
  0

• raw h5ad OR filtered h5ad

  #378 opened 4 months ago by elegantmedstu
  1

• load_anndata_from_input_and_output: retain_input_metadata input to nowhere

  #380 opened 4 months ago by benemead
  0

• Computing the output in asynchronous chunks in parallel takes longer than 144 hours

  #362 opened 7 months ago by Erhei130
  1

• Mismatch between summary for algorithm convergence and learning curve

  #377 opened 5 months ago by KaczorowskiLab
  0

• Increased number of UMIs per barcode after running remove-background

  #376 opened 5 months ago by hhvu0102
  1

• CellBender for .BAM file

  #375 opened 5 months ago by jzheng25
  0

• RuntimeError: CUDA driver error: invalid argument - Google Container Registry (GCR)

  #374 opened 5 months ago by AClab-sgarcia
  0

• Fixed Single cell RNA seq

  #372 opened 6 months ago by archana433
  1

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

  #370 opened 6 months ago by njbernstein
  0

• New fileformat output from BD rhapsody

  #359 opened 7 months ago by MelanieRN
  1

• Importance of model loss

  #366 opened 7 months ago by ShadHOH
  0

• Can't Computing target noise counts per gene for MCKP estimator

  #365 opened 7 months ago by Deroline10
  1

• Index Error in priors.py

  #343 opened 9 months ago by Ratoncito
  2

• Never mind

  #364 opened 7 months ago by maxwellfinkelstein
  0

• Question about input h5 file

  #361 opened 7 months ago by Linxiaobuskiy
  1

• Number of cells after cellbender much more than number of cells from cellranger (filtered)

  #358 opened 7 months ago by pc2001
  0

• "Trying to use CUDA, " \ AssertionError: Trying to use CUDA, but CUDA is not available.

  #357 opened 8 months ago by shnsk1995
  0

• Numpy build failed when installing cell bender from source

  #355 opened 8 months ago by shnsk1995
  0

• ERROR: Could not build wheels for pyzmq, which is required to install pyproject.toml-based projects

  #344 opened 9 months ago by axiba053
  1

• How to run CellBender for a pooling library?

  #354 opened 8 months ago by tewengtong
  0

• Is it possible to adjust the priors so that cellbender can work with shallow-sequenced data?

  #353 opened 8 months ago by onurcanbektas
  0

• Problem installing cellbender

  #351 opened 8 months ago by marctormo
  2

• Cell Ranger 'Multiplexing Capture' feature type not recognised.

  #340 opened 9 months ago by jpintar
  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 9 months ago by Ratoncito
  1

• Fix readthedocs

  #346 opened 8 months ago by sjfleming
  1

• Feature: tool for users to rescue v0.3.1 runs and to re-compute output counts in general

  #349 opened 9 months ago by sjfleming
  1