This PR contains a particularly important fix in 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 https://github.com/nf-core/differentialabundance/pull/186
• Fix sample metadata table in the html report not paginating by @davidecarlson in https://github.com/nf-core/differentialabundance/pull/195
• Fix GSEA indent in report by @WackerO in https://github.com/nf-core/differentialabundance/pull/190
• Add optional scree plot to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/192
• Enable all genes for exploratory by @WackerO in https://github.com/nf-core/differentialabundance/pull/188
• Add DESeq text to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/193
• Added colors to volcano by @WackerO in https://github.com/nf-core/differentialabundance/pull/194
• Document correct RNAseq matrix usage by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/200
• Update DESeq2/Limma by @WackerO in https://github.com/nf-core/differentialabundance/pull/201
• Add design to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/189
• Transcript lengths for DESeq2 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/203
• Release v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/204
• V1.4.0 fixes by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/206
• Dev -> master for v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/205

New Contributors

• @davidecarlson made their first contribution in https://github.com/nf-core/differentialabundance/pull/195

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.3.1…1.4.0

What’s Changed

• Post-release version bump by @WackerO in https://github.com/nf-core/differentialabundance/pull/181
• Correct Jon’s employer by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/182
• Fix logging for dendrograms by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/183
• Release v1.3.1 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/184
• Dev -> master for v1.3.1 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/185

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.3.0…1.3.1

What’s Changed

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

New Contributors

• @nf-core-bot made their first contribution in https://github.com/nf-core/differentialabundance/pull/121
• @ctuni made their first contribution in https://github.com/nf-core/differentialabundance/pull/128
• @smoe made their first contribution in https://github.com/nf-core/differentialabundance/pull/149
• @azedinez made their first contribution in https://github.com/nf-core/differentialabundance/pull/136

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.2.0…1.3.0

What’s Changed

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

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.1.1…1.2.0

What’s Changed

• V1.1.0 post release by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/87
• Sanitise for differential by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/89
• Release v1.1.1 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/90
• Dev -> master for v1.1.1 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/91

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.1.0…1.1.1

What’s Changed

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

New Contributors

• @apeltzer made their first contribution in https://github.com/nf-core/differentialabundance/pull/73

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.0.1…1.1.0

v1.0.1 - 2023-01-25

• [#49] - Add citation fixes, missing logos, output detail, and trigger Zenodo (@pinin4fjords, review by @apeltzer, @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, 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)