iRNA-COSI/APAeval

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Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples

Stars: 16
Forks: 14
Open beginner issues: 0
Indexed issues: 29

Dominant language: Python
License: MIT
Last GitHub push: Jan 11, 2024
Latest indexed: Sep 17, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

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29 open issues indexed

feat(Execution workflow): APA-Scan Open

snakemake

iRNA-COSI/APAeval#26 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 17, 2026
feat(Execution workflow): MISO Open

docker_container_available_on_Biocontainers

iRNA-COSI/APAeval#36 · 2 comments · 0 reactions · 2 assignees · Indexed Sep 17, 2026
feat(Execution workflow): Roar Open

docker_container_available_on_Biocontainers snakemake

iRNA-COSI/APAeval#38 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 17, 2026
docs: Check links Open

good first issue

iRNA-COSI/APAeval#42 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
docs: update participant contributions Open

documentation question

iRNA-COSI/APAeval#111 · 72 comments · 0 reactions · 3 assignees · Indexed Sep 17, 2026
test: Add genome fasta file to test_data directory Open

iRNA-COSI/APAeval#178 · 0 comments · 1 reaction · 2 assignees · Indexed Sep 17, 2026
feat(Utils): Add utilility to sort a BED file by chromosome and coordinate Open

iRNA-COSI/APAeval#186 · 0 comments · 1 reaction · 1 assignee · Indexed Sep 17, 2026
feat(Utils): add tool to convert reference PAS bed to gtf Open

enhancement

iRNA-COSI/APAeval#190 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
docs: prefer relative paths if possible Open

documentation good first issue low priority

iRNA-COSI/APAeval#192 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Utils): BAM to FASTQ Open

iRNA-COSI/APAeval#209 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
refactor: update Snakemake version in apaeval_env.yaml Open

enhancement low priority

iRNA-COSI/APAeval#223 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
fix(Execution workflow): APAtrap input parameter boolean check Open

bug

iRNA-COSI/APAeval#244 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
feat(Execution workflow):Time and memory usage Open

iRNA-COSI/APAeval#270 · 1 comment · 0 reactions · 2 assignees · Indexed Sep 17, 2026
feat(Publication): Plot outside of OpenEBench Open

duplicate

iRNA-COSI/APAeval#290 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Summary workflows): Differential summary workflow Open

low priority

iRNA-COSI/APAeval#294 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Summary workflow): Utils script/module to filter and convert ground truth TPM data to be compatible with relative quantification benchmark Open

high priority

iRNA-COSI/APAeval#301 · 3 comments · 0 reactions · 3 assignees · Indexed Sep 17, 2026
chore(CommBench): Meta issue Open

manuscripts meta

iRNA-COSI/APAeval#335 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Summary workflows): new SWF for relative usage quantification Open

meta

iRNA-COSI/APAeval#371 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
docs(Execution workflow): update output file specifications for reporting region-level 'polyA site usage scores' Open

documentation

iRNA-COSI/APAeval#380 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
feat(Execution workflow): CSI-UTR - report Format 04 BED file in workflow (per-PAS fractional relative usage) Open

iRNA-COSI/APAeval#388 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
docs(Summary Workflows): Logging Open

documentation good first issue low priority

iRNA-COSI/APAeval#394 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
fix(Summary workflows): don't overwrite previous results on new run Open

bug low priority nextflow

iRNA-COSI/APAeval#400 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Execution workflow): LABRAT feature to reuse previous makeTFfasta output Open

enhancement low priority

iRNA-COSI/APAeval#406 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
refactor: Singularity from conda environment might cause errors Open

low priority

iRNA-COSI/APAeval#418 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 17, 2026
chore: remove unnecessary requirement in identification swf Open

low priority

iRNA-COSI/APAeval#456 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Execution workflows / Utils): making RefSeq annotations work for QAPA and PAQR. Open

blocked enhancement

iRNA-COSI/APAeval#457 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Summary workflow): check that PAS are reported as single nucleotide in input bed Open

enhancement

iRNA-COSI/APAeval#458 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
chore: migrate containers from dockerhub.io/apaeval to biocontainers Open

iRNA-COSI/APAeval#467 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
feat(Summary workflow): additional annotation dependent metrics Open

enhancement low priority

iRNA-COSI/APAeval#468 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026

iRNA-COSI/APAeval

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