The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- [#97] - Allow for subsetting of samples for specific contrasts (@pinin4fjords, reported by @danhalligan-hx, review by @WackerO)
- [#105] - Enabled multiple GMT/GMX files for GSEA (@WackerO, reported by @grst, review by @pinin4fjords)
- [#108] - Add shiny app generation (starting feature set) (@pinin4fjords, review by @WackerO)
- [#110] - Add shiny app outputs to tower.yml (@pinin4fjords, review by @WackerO, @maxulysse)
- [#95] - Pipeline doesn't check for gene sets file specification when GSEA is activated (@pinin4fjords, reported by @danhalligan-hx, review by @FriederikeHanssen)
- [#93] - Shouldn't be re-using the single exploratory palette across multiple informative variables (@pinin4fjords, review by @matthdsm)
- [#89] - Sanitise for differential (@pinin4fjords, review by @WackerO)
- [#63] - Add git CI matrix for different test profiles to run (@WackerO, review by @pinin4fjords)
- [#60] - Add Affymetrix analysis modules, observation_name_col, make GTF optional, closing [#47], [#46], [#66] (@pinin4fjords, review by @apeltzer)
- [#70] - Array integration final bits: density plot improvement, output paths (@pinin4fjords, review by @matthdsm, @WackerO)
- [#55] - Don't drop dimensions in report with single informative variable (@pinin4fjords, review by @mashehu)
- [#57] - Update module shinyngs/validatefomcomponents and bump other shinyngs modules to resolve [#56] (@WackerO, review by @pinin4fjords)
- [#65] - Update shinyngs modules to latest to resolve palette issues reported by @Shellfishgene (@pinin4fjords, review by @mashehu)
- [#67] - Error when contrast is blocking by multiple variables (@pinin4fjords, reported by @clstacy, review by @jfy133)
- [#71] - Add palette options, bring full check.names fixes from upstream, closing [#68] reported by @Shellfishgene, [#69] reported by @clstacy. (@pinin4fjords, reported by @clstacy, review by @matthdsm, @WackerO)
- [#73] - Make
--matrix,--input,--featuresaccept either CSV,TXT or TSV files as input (@apeltzer, review by @pinin4fjords) - [#75] - Bump deseq2/differential for check.names fix (@pinin4fjords, review by @apeltzer)
- [#76] - Fix up non-gtf operation using matrix as annotation source (@pinin4fjords, reported by @apeltzer, review by @apeltzer)
- [#82] - Address v1.1.0 pre-release feedback (subway map fixes) (@pinin4fjords, reported by @mashehu)
- [#49 - Add citation fixes, missing logos, output detail, and trigger Zenodo (@pinin4fjords, review by @apeltzer, @jfy133)
Initial release of nf-core/differentialabundance, created with the nf-core template.
- [#1] - Set up initial modules, define and validate workflow inputs (@pinin4fjords, review by @WackerO)
- [#4] - Add input checking (@pinin4fjords, review by @WackerO)
- [#5] - Add differential analysis (@pinin4fjords, review by @WackerO)
- [#6] - Add exploratory plotting (@pinin4fjords, review by @WackerO)
- [#7] - Add differential plotting (@pinin4fjords, review by @WackerO)
- [#8] - Establish outputs/ reports (@pinin4fjords, review by @WackerO)
- [#12] - Handle spike sequences correctly (@pinin4fjords, review by @WackerO)
- [#15] - Add filtering module (@pinin4fjords, review by @WackerO)
- [#21] - Gene set analysis (@pinin4fjords, review by @WackerO)
- [#22] - Complete docs- README etc (@pinin4fjords, review by @WackerO)
- [#23] - Complete minimal report content (@pinin4fjords, review by @WackerO)
- [#38] - Complete full-size test data setup (@pinin4fjords, review by @WackerO)
- [#41] - Update citations (@pinin4fjords, review by @WackerO)