broadinstitute/CellBender issues and pull requests

#177 - solved

Issue - State: closed - Opened by jessicaliu70 over 1 year ago

#176 - How does cellbender call cells? What is the difference to cellranger?

Issue - State: closed - Opened by cheng-xiaoxiaoo over 1 year ago - 1 comment
Labels: user question

#175 - Windows Problems installing

Issue - State: open - Opened by kaylinker almost 2 years ago - 5 comments
Labels: user question

#174 - 10x H5 loading Error

Issue - State: closed - Opened by llumdi almost 2 years ago - 9 comments

#173 - How to check whether cellbender might have overcorrected the count matrix?

Issue - State: closed - Opened by Jiayi-Zheng almost 2 years ago - 2 comments
Labels: user question

#172 - Bump version in setup.py to match latest release

Pull Request - State: closed - Opened by prete almost 2 years ago - 2 comments

#171 - Support for pytorch running on Apple silicon processors

Issue - State: open - Opened by jopeptid almost 2 years ago - 16 comments

#170 - All droplets called as cells with a probability of 1

Issue - State: closed - Opened by djlmt almost 2 years ago - 4 comments

#169 - cellbender failing on sample with ~150 cells

Issue - State: closed - Opened by ktpolanski almost 2 years ago - 3 comments
Labels: bug

#168 - cellbender seems to idle after epoch calculation

Issue - State: closed - Opened by Dimmiso almost 2 years ago - 6 comments
Labels: enhancement

#167 - Use of CellBender for scATACseq data?

Issue - State: open - Opened by JeGrundman almost 2 years ago - 13 comments
Labels: enhancement

#166 - Are AnnData input files officially supported?

Issue - State: closed - Opened by tomsing1 almost 2 years ago - 6 comments

#165 - Fix readthedocs CSS

Pull Request - State: closed - Opened by sjfleming almost 2 years ago

#164 - Error importlib-metadata package

Issue - State: closed - Opened by ccruizm almost 2 years ago - 6 comments

#163 - Results interpretation - overestimation?

Issue - State: closed - Opened by giorgiatosoni almost 2 years ago - 24 comments

#162 - CUDA device busy or not available when other processes are running on the same node

Issue - State: closed - Opened by edg1983 almost 2 years ago - 9 comments

#161 - Running CellBender without graphic card

Issue - State: closed - Opened by nadinegheziel almost 2 years ago - 2 comments

#160 - How can I request cellbender to limit/use more threads/cores?

Issue - State: closed - Opened by angelasanzo almost 2 years ago - 8 comments
Labels: enhancement

#159 - 0.3.0 version download

Issue - State: closed - Opened by Irisapo almost 2 years ago - 2 comments

#158 - How to check which cells are removed after cellbender?

Issue - State: closed - Opened by devenderarora almost 2 years ago - 3 comments
Labels: user question

#157 - get cellbender version from command line

Issue - State: closed - Opened by edgano about 2 years ago - 2 comments
Labels: enhancement

#156 - publish to PyPI or conda ?

Issue - State: closed - Opened by jkanche about 2 years ago - 2 comments
Labels: enhancement

#155 - Implementation in scvi-tools

Issue - State: open - Opened by adamgayoso about 2 years ago - 4 comments

#154 - Unable to save plot

Issue - State: closed - Opened by williamwuyulu about 2 years ago - 2 comments

#153 - Log says "Preparing to write outputs to file..." but hours later, no output.

Issue - State: closed - Opened by julietluft about 2 years ago

#152 - How to get the fraction of count removed by CellBender for each gene

Issue - State: closed - Opened by sanchezy about 2 years ago - 1 comment
Labels: user question

#151 - Cell probabilities' output interpretation

Issue - State: closed - Opened by learning-MD about 2 years ago - 11 comments

#150 - length of the barcode

Issue - State: closed - Opened by xul0621 about 2 years ago - 5 comments
Labels: bug

#149 - "Cuda" counterpart for Apple M1 computers

Issue - State: open - Opened by areyoukidneyme about 2 years ago - 25 comments
Labels: enhancement

#148 - ImportError: DLL load failed while importing defs: The specified procedure could not be found.

Issue - State: open - Opened by areyoukidneyme about 2 years ago - 3 comments

#147 - How are priors calculated?

Issue - State: closed - Opened by apredeus about 2 years ago - 5 comments

#146 - Readthedocs broken

Issue - State: closed - Opened by apredeus about 2 years ago - 4 comments
Labels: bug, docs

#145 - Error Loading CellBender v3alpha H5 output in R

Issue - State: closed - Opened by samuel-marsh about 2 years ago - 6 comments
Labels: docs

#144 - Fail to Find Empty Droplets

Issue - State: closed - Opened by ZTYyy about 2 years ago - 2 comments

#143 - Shrink docker image with micromamba

Issue - State: open - Opened by sjfleming about 2 years ago - 1 comment
Labels: enhancement

#142 - Python API?

Issue - State: open - Opened by cnk113 about 2 years ago - 4 comments
Labels: enhancement

#141 - IndexError with remove-background

Issue - State: closed - Opened by karlann about 2 years ago - 7 comments

#140 - input a raw feature count but the qc html shows UMI counts as if it were a filtered feature count

Issue - State: closed - Opened by JiajiaChen1 about 2 years ago - 2 comments
Labels: user question

#139 - The output csv file is hdf5

Issue - State: closed - Opened by katiesaund about 2 years ago - 1 comment

#138 - output.h5 and output_filtered.h5 files are identical

Issue - State: closed - Opened by katiesaund about 2 years ago - 1 comment
Labels: user question

#137 - what to put in expected cells and total droplets?

Issue - State: closed - Opened by dm8000 about 2 years ago - 2 comments

#136 - use kde instead of hist, and other tweaks

Pull Request - State: closed - Opened by jamestwebber about 2 years ago

#135 - use of eval considered harmful, frightening

Pull Request - State: closed - Opened by jamestwebber about 2 years ago - 5 comments

#134 - Cell probability question

Issue - State: closed - Opened by PalatinTech over 2 years ago - 2 comments
Labels: user question

#133 - create new 0.2.1 release ?

Issue - State: closed - Opened by arielzn over 2 years ago - 2 comments

#132 - Feature request: Include expected contamination proportion as input

Issue - State: open - Opened by wmacnair over 2 years ago - 3 comments
Labels: enhancement

#131 - filtered.h5 matrix is strange

Issue - State: closed - Opened by baigal628 over 2 years ago - 2 comments

#128 - read_10x_h5 error in scanpy 1.9.1

Issue - State: closed - Opened by francois-a over 2 years ago - 15 comments

#127 - CUDA busy error when running cellbender on slurm

Issue - State: closed - Opened by edg1983 over 2 years ago - 5 comments

#126 - Make an output metrics file and update the WDL

Issue - State: closed - Opened by sjfleming over 2 years ago - 2 comments
Labels: enhancement

#125 - Update docs to include versions and version history

Issue - State: closed - Opened by sjfleming over 2 years ago - 2 comments
Labels: enhancement

#124 - Accept loom file format as input

Issue - State: closed - Opened by sjfleming over 2 years ago - 4 comments
Labels: enhancement

#123 - Running with python -m?

Issue - State: closed - Opened by bbimber over 2 years ago - 2 comments
Labels: enhancement

#121 - Can I use output from cellranger-arc in cellbender ?

Issue - State: open - Opened by hemantgujar over 2 years ago - 26 comments
Labels: bug, enhancement

#118 - Fix setup.py to include subpackages

Pull Request - State: closed - Opened by mxposed almost 3 years ago - 2 comments

#117 - CUDA not found

Issue - State: closed - Opened by MrDotOne almost 3 years ago - 6 comments

#116 - No empty droplets error when genes manually appended

Issue - State: closed - Opened by saxovocal almost 3 years ago - 2 comments
Labels: user question

#115 - Fix computation of when learning should be retried with lower learning rate.

Pull Request - State: closed - Opened by alecw almost 3 years ago - 8 comments

#114 - Does cellbender work with citeseq data?

Issue - State: closed - Opened by smk5g5 almost 3 years ago - 11 comments
Labels: enhancement

#112 - Report the UMIs in the filtered barcodes before/after ambient RNA correction?

Issue - State: closed - Opened by apredeus about 3 years ago - 2 comments
Labels: enhancement

#111 - Do not output "cells" with zero counts

Issue - State: open - Opened by sjfleming about 3 years ago - 3 comments
Labels: bug

#109 - Multiple GPU usage

Issue - State: open - Opened by vswarup about 3 years ago - 3 comments
Labels: refactoring

#108 - Cell Bender + RNA Velocity

Issue - State: open - Opened by samuel-marsh about 3 years ago - 1 comment

#106 - Cell Probability

Issue - State: closed - Opened by faraz89 about 3 years ago - 4 comments
Labels: user question

#101 - cellrender won't give any results

Issue - State: closed - Opened by FanBioinformatics over 3 years ago - 6 comments

#98 - Command line argument to limit posterior generation memory usage

Issue - State: open - Opened by sjfleming over 3 years ago - 2 comments
Labels: enhancement

#96 - Error running cellbender

Issue - State: closed - Opened by mxposed over 3 years ago - 4 comments

#95 - Example download issue

Issue - State: open - Opened by YubinXie over 3 years ago - 6 comments
Labels: enhancement

#94 - "No cells found! Cannot compute expected FPR." Error

Issue - State: closed - Opened by vincentnmiao over 3 years ago - 6 comments
Labels: user question

#89 - using multiple 10X runs to better estimate background and biological expression

Issue - State: closed - Opened by vitkl over 3 years ago - 3 comments

#83 - Documentation: details of the h5 output format and fields

Issue - State: closed - Opened by sjfleming almost 4 years ago - 1 comment
Labels: enhancement

#76 - Better prior for epsilon

Issue - State: closed - Opened by sjfleming almost 4 years ago

#75 - Better prior for rho - swapping fraction

Issue - State: closed - Opened by sjfleming almost 4 years ago

#67 - Batch size, CUDA out of memory

Issue - State: closed - Opened by Elhl93 about 4 years ago - 31 comments

#63 - Output contains droplets with 0 counts

Issue - State: open - Opened by henryjtaylor about 4 years ago - 3 comments
Labels: bug

#36 - HDF5 file output is not compatible with cellranger aggr v3

Issue - State: closed - Opened by whelena almost 5 years ago - 9 comments

#24 - Droplet Time Machine

Issue - State: open - Opened by mbabadi about 5 years ago

#5 - Comprehensive test suite

Issue - State: open - Opened by sjfleming about 5 years ago - 4 comments

#4 - Refactor SingleCellRNACountsDataset

Issue - State: closed - Opened by sjfleming about 5 years ago - 1 comment
Labels: refactoring

GitHub / broadinstitute/CellBender issues and pull requests