This PR contains a particularly important fix in [#20, which resolves a long-standing issue in proper usage of abundance values from the rnaseq workflow. Users can now take the lengths from that workflow (using rnaseq >=v3.13.2) and pass them to this workflow to account for transcript length biases across samples. ](https://github.com/nf-core/differentialabundance/pull/20, which resolves a long-standing issue in proper usage of abundance values from the rnaseq workflow. Users can now take the lengths from that workflow (using rnaseq >=v3.13.2) and pass them to this workflow to account for transcript length biases across samples. )

What’s Changed

• Post 1.3.1 release changes by @pinin4fjords in #186
• Fix sample metadata table in the html report not paginating by @davidecarlson in #195
• Fix GSEA indent in report by @WackerO in #190
• Add optional scree plot to report by @WackerO in #192
• Enable all genes for exploratory by @WackerO in #188
• Add DESeq text to report by @WackerO in #193
• Added colors to volcano by @WackerO in #194
• Document correct RNAseq matrix usage by @pinin4fjords in #200
• Update DESeq2/Limma by @WackerO in #201
• Add design to report by @WackerO in #189
• Transcript lengths for DESeq2 by @pinin4fjords in #203
• Release v1.4.0 by @pinin4fjords in #204
• V1.4.0 fixes by @pinin4fjords in #206
• Dev -> master for v1.4.0 by @pinin4fjords in #205

New Contributors

• @davidecarlson made their first contribution in #195

Full Changelog: 1.3.1…1.4.0

What’s Changed

• Post-release version bump by @WackerO in #181
• Correct Jon’s employer by @pinin4fjords in #182
• Fix logging for dendrograms by @pinin4fjords in #183
• Release v1.3.1 by @pinin4fjords in #184
• Dev -> master for v1.3.1 by @pinin4fjords in #185

Full Changelog: 1.3.0…1.3.1

What’s Changed

• Bump versions after 1.2.0 release by @pinin4fjords in #114
• Fix low replication by @pinin4fjords in #117
• Template update for nf-core/tools v2.8 by @pinin4fjords in #124
• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in #121
• Add spaces to satisfy nf-core download for singularity by @pinin4fjords in #126
• Posible fix for issue #127 by @ctuni in #128
• Module updates to fit with recent registry changes by @pinin4fjords in #129
• document reasons for lack of differential expression by @pinin4fjords in #130
• Improve gtf to table configurability by @pinin4fjords in #131
• Updated Deseq2 params by @WackerO in #137
• Fix control_features and sizefactors_from_controls by @WackerO in #144
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #145
• Fix up sample exclusion options by @pinin4fjords in #132
• Update README.md - add ref to nf-core/rnaseq and Affymetrix by @smoe in #149
• Update modules by @WackerO in #151
• Trivial change, not even a typo: Update README.md - Inserted missing blank. by @smoe in #146
• Updated env versions of rmarkdownnotebook by @WackerO in #154
• Soft matrix support by @azedinez in #136
• Template update 2.10 - conflicts solving by @WackerO in #160
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #158
• Correct typo by @pinin4fjords in #162
• Point to shinyngs example in docs by @pinin4fjords in #161
• Module update: matrixfilter by @WackerO in #159
• Rlog + other small fixes by @pinin4fjords in #164
• Add proteus module for maxquant data analysis by @WackerO in #147
• Output notebook by @pinin4fjords in #167
• Affy docs by @pinin4fjords in #169
• Update metro map by @pinin4fjords in #172
• Deseq2 tip by @pinin4fjords in #173
• Fix metro map by @pinin4fjords in #174
• Don’t use contrasts directly from the input channel by @pinin4fjords in #175
• Bump shinyngs by @pinin4fjords in #176
• Release v1.3.0 by @pinin4fjords in #177
• Removed shiny error for proteus runs by @WackerO in #179
• v1.3.0 post-review by @pinin4fjords in #180
• Dev -> master for v1.3.0 by @pinin4fjords in #178

New Contributors

• @nf-core-bot made their first contribution in #121
• @ctuni made their first contribution in #128
• @smoe made their first contribution in #149
• @azedinez made their first contribution in #136

Full Changelog: 1.2.0…1.3.0

What’s Changed

• Bump versions after 1.1.1 bugfix release by @pinin4fjords in #92
• Warn missing gene sets by @pinin4fjords in #96
• use color scales appropriate to variable, apply upstream palette fixes by @pinin4fjords in #94
• Update differential module interface, add pre-contrast subsetting options by @pinin4fjords in #103
• Enabled multiple GMT/GMX files for GSEA by @WackerO in #105
• Add shinyngs app creation and deployment by @pinin4fjords in #107
• Add shinyngs outputs to Tower reports by @pinin4fjords in #110
• Release v1.2.0 by @pinin4fjords in #111
• Pre v1.2.0 fixes by @pinin4fjords in #113
• Dev -> master for v1.2.0 by @pinin4fjords in #112

Full Changelog: 1.1.1…1.2.0

What’s Changed

• V1.1.0 post release by @pinin4fjords in #87
• Sanitise for differential by @pinin4fjords in #89
• Release v1.1.1 by @pinin4fjords in #90
• Dev -> master for v1.1.1 by @pinin4fjords in #91

Full Changelog: 1.1.0…1.1.1

What’s Changed

• V1.0.1 post release by @pinin4fjords in #53
• Don’t drop dimensions in report with single informative variable by @pinin4fjords in #55
• [Module update] Validatefomcomponents by @WackerO in #58
• Update shinyngs modules to latest to resolve palette issues by @pinin4fjords in #65
• Attempted fix for multiple blocking variables by @pinin4fjords in #64
• [Git CI] Add test matrix by @WackerO in #63
• Add Affymetrix analysis modules, observation_name_col, make GTF optional by @pinin4fjords in #60
• Array integration final bits: density plot, output paths by @pinin4fjords in #70
• Add palette options, bring full check.names fixes from upstream by @pinin4fjords in #71
• Add metro map for workflow by @pinin4fjords in #72
• Add fix for csv/tsv/etc by @apeltzer in #73
• fix typo in subway, remove misplaced station dot by @pinin4fjords in #74
• Bump deseq2/differential for check.names fix by @pinin4fjords in #75
• Fix up non-gtf operation using matrix as annotation source by @pinin4fjords in #76
• Release v1.1.0 by @pinin4fjords in #77
• Resolve tiny conflict in release PR. by @pinin4fjords in #79
• Resolve tiny conflict in release PR (attempt 2) by @pinin4fjords in #80
• Dev -> master for v1.1.0 by @pinin4fjords in #78
• Address v1.1.0 pre-release feedback (subway map fixes) by @pinin4fjords in #82
• Dev -> master with subway fixes by @pinin4fjords in #86

New Contributors

• @apeltzer made their first contribution in #73

Full Changelog: 1.0.1…1.1.0

v1.0.1 - 2023-01-25

• [#49] - Add citation fixes, missing logos, output detail, and trigger Zenodo ([@pinin4fjords](https://github.com/pinin4fjords), review by [@apeltzer](https://github.com/apeltzer), [@jfy133](https://github.com/jfy133))

v1.0.0 - 2023-01-23

Initial release of nf-core/differentialabundance, created with the nf-core template.

Added

• [#1] - Set up initial modules, define and validate workflow inputs ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#4] - Add input checking ([@pinin4fjords](https://github.com/pinin4fjords), , review by [@WackerO](https://github.com/WackerO))
• [#5] - Add differential analysis ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#6] - Add exploratory plotting ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#7] - Add differential plotting ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#8] - Establish outputs/ reports ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#12] - Handle spike sequences correctly ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#15] - Add filtering module ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#21] - Gene set analysis ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#22] - Complete docs- README etc ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#23] - Complete minimal report content ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#38] - Complete full-size test data setup ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
• [#41] - update citations ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))