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Peak annotation & enrichment #142

Merged
merged 33 commits into from
Nov 8, 2023
Merged

Peak annotation & enrichment #142

merged 33 commits into from
Nov 8, 2023

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Nov 7, 2023 •
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Changes

New processes

  • findMotifsGenome command in Homer
  • ame command in MEME
  • peak annotation with chipseeker

Issues

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
  • [ ] Update docs if there are any API changes. on hold until before public release
  • If a new nextflow process is implemented, define the process container and stub.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kelly-sovacool
feat: add process for motifs w/ HOMER
074af00
@kelly-sovacool
feat: add process for HOMER findMotifsGenome
4f4d518
@kelly-sovacool
fix: use nciccbr homer container
b5e9c42
@kelly-sovacool
fix: nomotif param name
cf74113
@kelly-sovacool
feat: save genome gtf files for custom genomes
f45a891
@kelly-sovacool
feat: pass in genome fasta to homer
fe1ae5a
@kelly-sovacool
feat: add de_novo param for homer
54f2c25
@kelly-sovacool
feat: use jaspar db for homer known motifs
9738df6
@kelly-sovacool
refactor: format meta.id to be sample basename after consensus calling
546fd62
@kelly-sovacool
feat: write process for MEME AME
2ca3151
@kelly-sovacool
fix: typo
0a2acf6
@kelly-sovacool
fix: join list of peak files
5529831
@kelly-sovacool
fix: typo in container name
62d1981
@kelly-sovacool
feat: add script to annotate peaks from ASPEN
7533f8e 
source: https://github.com/CCBR/ASPEN/blob/55f909d76500c3502c1c397ef3000908649b0284/workflow/scripts/ccbr_annotate_peaks.R
@kelly-sovacool
feat: use meme motif tars from ASPEN
3155f0a
@kelly-sovacool
feat: run MEME AME successfully
35df682
@kelly-sovacool
docs: update changelog with homer & meme
817e996
@kelly-sovacool
chore: link to source
d332bb9
@kelly-sovacool
chore: run styler
7c86fed
@kelly-sovacool
fix: only try to create log dir if DNE
d8c4898
@kelly-sovacool
fix: designate annotate_peaks.R as an Rscript
c7c1e79
@kelly-sovacool
feat: run chipseeker on consensus peaks
6d3ad09
@kelly-sovacool
feat: option to skip chipseeker
5e4270c 
e.g. in case genome isn't supported by txdb
@kelly-sovacool
fix: only run chipseeker on narrowpeak files
118be53 
may need to modify broadpeak files to be able to run chipseeker...
@kelly-sovacool kelly-sovacool changed the title Implement processes for Homer findMotifsGenome and MEME AME Peak annotation & enrichment Nov 8, 2023
@kelly-sovacool kelly-sovacool merged commit 6d54d40 into main Nov 8, 2023
2 checks passed
@kelly-sovacool kelly-sovacool deleted the motifs branch November 8, 2023 18:31
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motif enrichment analysis (ame) with MEME Annotate peaks with chipseeker Identify motifs w/ HOMER
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@kelly-sovacool