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cellranger multi => MTX_TO_H5AD: input file name collision
bug
Something isn't working
#383
opened Oct 17, 2024 by
nick-youngblut
Crashes due to trying to unzip file that is not zipped
bug
Something isn't working
#380
opened Oct 11, 2024 by
esrice
CellRanger Multi => add combined h5ad files in New feature or request
mtx_conversions
enhancement
#378
opened Oct 8, 2024 by
nick-youngblut
CellRanger Multi => add to MultiQC report
enhancement
New feature or request
#377
opened Oct 8, 2024 by
nick-youngblut
cellranger multi => pipeline creates STAR index that does not match probeset
bug
Something isn't working
#375
opened Oct 7, 2024 by
nick-youngblut
cellrangerarc test failing - null path?
bug
Something isn't working
#374
opened Oct 4, 2024 by
davhum
cellranger-multi => incorrect feature_type assigned to samples
bug
Something isn't working
#373
opened Oct 3, 2024 by
nick-youngblut
Allow pre-built cellranger index, CellrangerARC index, simpleaf Index, and simpleaf tx2pgene load from igenomes.json
enhancement
New feature or request
#371
opened Sep 20, 2024 by
wzheng0520
MTX_TO_H5AD module cannot take ch_star_index
bug
Something isn't working
#370
opened Sep 20, 2024 by
wzheng0520
results from awsmegatests missing on homepage
bug
Something isn't working
#367
opened Sep 2, 2024 by
asp8200
test_full-profile not running out-of-the-box
bug
Something isn't working
#366
opened Sep 2, 2024 by
asp8200
Standardize h5ad/seurat var gene annotations across aligners
enhancement
New feature or request
#363
opened Aug 15, 2024 by
alexblaessle
nextflow inspect does not work due to missing parameters
bug
Something isn't working
#347
opened Jul 26, 2024 by
stevekm
cellranger count => Your reference does not contain the expected files
bug
Something isn't working
#345
opened Jul 11, 2024 by
nick-youngblut
Implement sample demultiplexing followed by VDJ + feature barcode analysis per sample
enhancement
New feature or request
#343
opened Jun 28, 2024 by
herpov
cellranger_count.py: capture stderr and stdout
enhancement
New feature or request
quality & consistency
improve quality and reduce maintenance burden
#341
opened Jun 24, 2024 by
nick-youngblut
Trimming R1 fast files in all aligners
enhancement
New feature or request
#333
opened May 24, 2024 by
ChristopherMancuso
cellranger-multi implementation follow-up
enhancement
New feature or request
#332
opened May 23, 2024 by
fmalmeida
5 tasks
Running 'cellranger-arc count' with existing genome index
enhancement
New feature or request
#331
opened May 17, 2024 by
ashwinikumarkulkarni
Sample merging does not work if files are named the same
bug
Something isn't working
bug-confirmed
#324
opened May 4, 2024 by
nick-youngblut
cellranger mkref with multiple species
enhancement
New feature or request
#319
opened Apr 16, 2024 by
MaestSi
cellranger_count.py: remove any existing output directory
enhancement
New feature or request
#315
opened Apr 9, 2024 by
nick-youngblut
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