Recent Releases of differentialabundance
differentialabundance - v1.5.0 - 2024-05-08
Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.5.0...1.5.0
- Nextflow
Published by WackerO over 1 year ago
differentialabundance - v1.4.0 - 2023-11-27
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
- Nextflow
Published by pinin4fjords about 2 years ago
differentialabundance - v1.3.1 - 2023-10-26
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
- Nextflow
Published by pinin4fjords about 2 years ago
differentialabundance - v1.3.0 - 2023-10-24
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 controlfeatures and sizefactorsfrom_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
- Nextflow
Published by pinin4fjords about 2 years ago
differentialabundance - v1.2.0 - 2023-04-19
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
- Nextflow
Published by pinin4fjords over 2 years ago
differentialabundance - v1.1.1 - 2023-03-02
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
- Nextflow
Published by pinin4fjords almost 3 years ago
differentialabundance - v1.1.0 - 2023-02-22
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, observationnamecol, 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
- Nextflow
Published by pinin4fjords almost 3 years ago
differentialabundance - nf-core/differentialabundance v1.0.1
v1.0.1 - 2023-01-25
- [#49] - Add citation fixes, missing logos, output detail, and trigger Zenodo (@pinin4fjords, review by @apeltzer, @jfy133)
- Nextflow
Published by pinin4fjords almost 3 years ago
differentialabundance - nf-core/differentialabundance v1.0.0
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)
- Nextflow
Published by pinin4fjords almost 3 years ago