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28 Open 20 Closed
28 Open 20 Closed
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Issues list

m4/ax_r_package.m4 is outdated
#59 opened May 28, 2022 by rekado 1.1.9
new version of star will break the pipeline
#57 opened Mar 8, 2021 by frenkiboy 1.1.9
convert_matrix_from_mtx_to_loom:102 - ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements
#56 opened Sep 12, 2020 by smoe
check for corresponding chromosome names in GTF and fasta feature
#53 opened Jul 19, 2020 by frenkiboy
Local pipeline install fails during convert_matrix_from_mtx_to_loom.py
#52 opened Jun 30, 2020 by t-carroll
3
loom2sce should be called only once enhancement New feature or request feature
#51 opened May 9, 2020 by frenkiboy
STAR breaks mm Matrix format for Velocyto output bug Something isn't working
#50 opened Apr 16, 2020 by frenkiboy
@frenkiboy
Pipeline dies on sort bam step if tmp files exist feature
#49 opened Mar 23, 2020 by frenkiboy
Add whitelist option to the pipeline
#47 opened Jan 29, 2020 by frenkiboy
FastqToSAM complains if header contains barcode
#43 opened Aug 3, 2018 by frenkiboy
Add number of cells per experiment to the report
#42 opened Aug 1, 2018 by frenkiboy
Rename slots in single cell experiment to standardly used names
#41 opened Jul 27, 2018 by frenkiboy
check whether the genome is defined
#38 opened Jun 4, 2018 by frenkiboy
Settings parsing - more descriptive error messages
#37 opened Jun 4, 2018 by frenkiboy
Verbosely describe how to contribute
#36 opened Jun 4, 2018 by frenkiboy
check whether the output directory is writeable
#33 opened May 29, 2018 by frenkiboy
make iSEE/singleCellTK package work nicely with sce object produced by the pipeline
#29 opened May 23, 2018 by frenkiboy
1
test pipeline with R3.5 and updated packages
#28 opened May 23, 2018 by frenkiboy
add barcode error correction enhancement New feature or request
#26 opened Apr 18, 2018 by frenkiboy
Redirect noisy output to log file
#24 opened Mar 22, 2018 by Blosberg
--printshellcmds not working
#23 opened Mar 22, 2018 by Blosberg
Log file output not going through on SM jobs on the cluster
#22 opened Mar 22, 2018 by Blosberg
add mitochondrial RNA contamination estimation enhancement New feature or request
#21 opened Mar 16, 2018 by frenkiboy
Develop indrops parser enhancement New feature or request
#20 opened Mar 15, 2018 by frenkiboy
Add report description
#16 opened Feb 20, 2018 by frenkiboy
ProTip! Adding no:label will show everything without a label.