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Issues list

add LRT as an option to DESeq2 enhancement RNA-seq
#1097 opened Apr 15, 2025 by katsikora
@katsikora
ValueError: 'group' is not in list bug RNA-seq
#1094 opened Mar 20, 2025 by malszycki
2
HiC - enzyme HiC
#1093 opened Mar 2, 2025 by hanrong498
@katsikora
4
add summary of whatshap splitting metrics RNA-seq
#1091 opened Jan 28, 2025 by katsikora
@katsikora
cleanup code
#1087 opened Jan 14, 2025 by katsikora
1 of 4 tasks
@katsikora
RuleException in rule validateFQ: The name 'snakePipes_cluster_logDir' is unknown in this context snakemake
#1084 opened Dec 31, 2024 by sunta3iouxos
2
pairtools - multiqc enhancements
#1081 opened Nov 15, 2024 by WardDeb
@WardDeb
force compression of multiqc_data enhancement question
#1079 opened Nov 9, 2024 by thomasmanke
@WardDeb
three-prime-seq replace "shell" with "script" directive bug RNA-seq
#1078 opened Nov 8, 2024 by katsikora
proper envs - conda versions
#1077 opened Nov 7, 2024 by WardDeb
salmonIndex seq name from genes_bed2fasta
#1076 opened Oct 29, 2024 by hanrong498
rule histoneHMM_out_gz throws an error at workflow rerun in the same output folder bug ChIP-Seq
#1070 opened Oct 18, 2024 by katsikora
snakepipes - pypi installation/configuration
#1069 opened Oct 10, 2024 by WardDeb
@WardDeb
makePairs workflow cleanup
#1068 opened Oct 9, 2024 by WardDeb
5 tasks
@caballero
1
Clean up global args
#1066 opened Oct 9, 2024 by WardDeb
default conda env in 3.0.0
#1061 opened Sep 25, 2024 by sunta3iouxos
5
bowtie --cutntag -X 700, ATAC-seq, maxfragment size
#1057 opened Sep 10, 2024 by sunta3iouxos
shift read correction for ATAC/Cut&Tag
#1056 opened Sep 10, 2024 by sunta3iouxos
error while running the DNA-mapping
#1045 opened Sep 3, 2024 by sunta3iouxos
3
dependency issues wgbs
#1044 opened Sep 3, 2024 by sunta3iouxos
3
error in samtools sort
#1021 opened Jul 22, 2024 by sunta3iouxos
3
error while creating the environment using the git devel
#1020 opened Jul 18, 2024 by sunta3iouxos
1
human reference genome, no_alt and PARY
#1018 opened Jul 15, 2024 by sunta3iouxos
2
snakePipes createEnvs fails
#1016 opened Jun 13, 2024 by musikutiv
1
allow user to specify mincount for filtering windows for DB with CSAW ATAC-seq ChIP-Seq External Tool An update/modification of an external tool is needed
#1014 opened Apr 23, 2024 by katsikora
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