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63 Open 88 Closed
63 Open 88 Closed
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Issues list

FDR cutoff alpha not applied in rnaseq.Rmd
#422 opened Dec 3, 2024 by Mira0507
use fasterq-dump
#409 opened Oct 8, 2024 by daler
SRA runs should save data elsewhere and then symlink
#408 opened Oct 8, 2024 by daler
Layout rather than LibraryLayout
#407 opened Oct 8, 2024 by daler
2
move strandedness in params
#405 opened Oct 8, 2024 by daler
Add hyperlink to rnaseq.Rmd error message, 'duplicate names found after removing pattern ^contr_[^_]+_'
#395 opened Nov 28, 2023 by menoldmt
1
1
In functional-enrichment.Rmd and gene-patterns.Rmd, add config for turning on/off lazy caching
#391 opened Aug 16, 2023 by menoldmt
1
Automatic plot resizing in gene-patterns
#390 opened Aug 16, 2023 by menoldmt
Add Functional Enrichment TSV Links to functional-enrichment.Rmd
#389 opened Aug 16, 2023 by menoldmt
Typographical errors in Gene-Patterns Explanatory Text
#388 opened Aug 16, 2023 by menoldmt
In gene-patterns.Rmd, ensure factors for certain colData used in gene patterns
#387 opened Aug 16, 2023 by menoldmt
PDF plots in gene-patterns.Rmd
#386 opened Aug 16, 2023 by menoldmt
consider using black/greylists for peak-calling
#381 opened Jul 17, 2023 by daler
Document reference configs docs
#355 opened Jan 10, 2022 by kcampbell824
@kcampbell824
proposal to reorganize output directories
#352 opened Oct 13, 2021 by daler
Catch "Valid Key Exception" in Functional Enrichment
#349 opened Oct 1, 2021 by fridells51
macs2 rule should handle PE better
#345 opened Sep 3, 2021 by daler
convert circleci tests to more easily run locally v1.10
#344 opened Aug 24, 2021 by daler
1
preflight reporting
#343 opened Aug 22, 2021 by daler
rm libsize table and rule v1.10
#342 opened Aug 22, 2021 by daler
fastq-dump arguments
#328 opened Jan 11, 2021 by daler
Issues with complex dataset
#310 opened Aug 18, 2020 by esnaultc
update zebrafish reference config
#296 opened Jun 5, 2020 by daler
Update plotMA.label in helpers rnaseq.rmd v1.6 Issues to address specifically for v1.6
#292 opened May 26, 2020 by mitraak
provide access to config files from within R
#284 opened May 11, 2020 by daler
ProTip! What’s not been updated in a month: updated:<2024-11-12.