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Commits on Aug 4, 2025

• docs: add explanations and sources to `config/config.yaml` (#162)

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Commits on Jul 23, 2025

• chore: update $schema in config.schema.yaml to `2020-12` (#161)

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Commits on Jul 21, 2025

• docs: provide hints where to check whether auto-detection worked (#160)

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• docs: mention that you can merge multiple GMT files for fgsea (#159)

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Commits on Jul 16, 2025

• docs: update breaking changes 3.0.0 (#158)

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Commits on Jul 15, 2025

• feat!: allow to run spia on multiple pathway databases (separately) (#157)

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• feat: switch to fastp for trimming (#155)

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• fix: set spia mem_mb to 32G and threads to 32 (#154)

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Commits on May 19, 2025

• fix: make isoformanalyzer annotation match transcriptome reference (#152)

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Commits on Apr 23, 2025

• fix: use `verify_integrity=True` in pandas `set_index()` for samples and units to check for duplicates (#149)

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• fix: make postprocess sorting work with more than one signed_pi value column (#150)

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Commits on Mar 19, 2025

• fix: move summing of go-term fold changes out of log-space (#141)

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Commits on Jun 25, 2024

• docs: improve base_level explanation in config.yaml files (#101)

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Commits on Jun 24, 2024

• docs: improve configs and configuration README.md (#99)

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Commits on Jun 13, 2024

• chore: update bioconductor-biomart to 2.58 (#89)

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• perf: datavzrd wrapper `v3.12.1`, offer-excel configurable, free disk space for CI, dynamic sleuth_init mem_mb, pure download rules as localrules (#92)

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Commits on Mar 20, 2024

• chore: update datavzrd to latest version v3.5.2 (#90)

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Commits on Jan 31, 2024

• perf: improve spia script and report (#83)

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Commits on Jan 30, 2024

• fix: canonical transcript mapped read extraction (#77)

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Commits on Sep 14, 2023

• fix: simpler three prime QuantSeq cutadapt setup (#78)

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Commits on Aug 16, 2023

• fix: update samtools.yaml to latest `1.17` and update github actions (#75)

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Commits on Feb 1, 2022

• adjust fgsea.R script to changes in fgsea() function interface (#55)

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Commits on May 17, 2021

• plot-bootstrap.R: fix script to handle an empty genes of interest list in config.yaml (#44)

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Commits on May 14, 2021

• automatically download reference (#43)

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Commits on May 11, 2021

• include Zenodo DOI (#42)

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• Migrate to new workflow usage (#41)

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Commits on Apr 8, 2021

• Extend p value plot captions (#29)

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Commits on Mar 4, 2021

• fgsea.r: unnest leadingEdge and create correct columns for empty data (#28)

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Commits on Sep 16, 2020

• ensure that biomart getBM() does not use a cache (this has led to failures) (#26)

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Commits on Aug 21, 2020

• remove .test/report.html as it is too big (17 Mb is > 10 Mb GitHub limit) (#25)

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Commits on Apr 9, 2020

• Bootstrap plots checkpoint to report directory (#21)

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Commits on Mar 4, 2020

• only remove sample rows with NAs in model-relevant columns, leave all other columns alone (#19)

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Commits on Mar 3, 2020

• fgsea.R: fix ext_gene ties equivalent to ens_gene ties in sleuth_diffexp, fix indenting (#18)

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• pin all uses of select() to the library, to avoid AnnotationDbi vs. dplyr collisions (#17)

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Commits on Mar 2, 2020

• enable any name for diffexp grouping column, remove bugs: case of no custom_transcripts, future-proof column selection (#13)

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