nf-core differentialabundance issues

nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

https://nf-co.re/differentialabundance

MIT License

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issues

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Create subworkflow for deconvolution analyses in bulk data

#361 apeltzer opened 6 days ago
0
Error with `ch_gene_sets` when running gprofiler analysis without gmt file

#360 Mathias-Boulanger opened 1 week ago
1
Add software versions in nf-test and check column presence in `.Rmd`

#359 atrigila closed 6 days ago
1
Unable to run pipeline – please provide test data

#358 febedtu opened 1 week ago
1
Fix tests; add version channels; remove params access in subworkflow

#357 bjlang closed 1 week ago
1
Replace unmaintained Proteus with maxLFQ, by author's suggestion.

#356 vmkalbskopf opened 1 week ago
0
Assess if we should simplify CUSTOM_TABULARTO GSEACLS

#355 nschcolnicov closed 1 week ago
2
Add a warning in the RMD report when some rows are lost after merging Diff and Fatures tables

#354 alanmmobbs93 closed 4 days ago
7
Importing Data into Chart Studio Cloud

#353 Faitero opened 1 week ago
0
Add nf-core module DoRothEA to nf-core/differentialabundance

#352 atrigila opened 1 week ago
0
Add nf-core module PROGENy to nf-core/differentialabundance

#351 atrigila opened 1 week ago
0
Add module decoupleR to nf-core/modules

#350 atrigila opened 1 week ago
1
Add module DoRothEA to nf-core/modules

#349 atrigila opened 1 week ago
0
Update test full profile

#348 nschcolnicov closed 1 week ago
6
Test full profile not working in dev

#347 nschcolnicov closed 1 week ago
1
Add plots by biotype

#346 atrigila closed 1 week ago
1
Gene name in differential and abundance tables

#345 oquendoM opened 2 weeks ago
0
Fix replacement of NA sub-strings in blocking variable

#344 atrigila closed 2 weeks ago
1
Add pipeline-level nf-tests

#343 atrigila closed 2 weeks ago
3
Fix report volcano plots

#342 WackerO closed 2 weeks ago
1
Create 'differential' subworkflow

#341 pinin4fjords opened 2 weeks ago
1
Volcano plot in report shows less genes than in 'plots/differential/*/png/volcano.png'

#340 d4straub closed 4 days ago
10
325 mixed model in limma

#339 KamilMaliszArdigen opened 2 weeks ago
10
Allow lfc_threshold to be a float

#338 vmkalbskopf opened 3 weeks ago
0
[dev-ratio] fix channels after the recent modules additions

#337 suzannejin opened 3 weeks ago
1
Dev ratio fix channels

#336 suzannejin closed 3 weeks ago
2
322 add module deseq2

#335 roskamsh closed 3 weeks ago
5
Dev ratio merge dev

#334 suzannejin closed 3 weeks ago
1
add GPROFILER2 module to ENRICHMENT subworkflow

#333 roskamsh closed 3 weeks ago
1
add additional reference to wiki article for MAD

#332 davidecarlson closed 2 weeks ago
3
[dev-ratio] add limma to test_experimental

#331 suzannejin closed 3 weeks ago
1
Remove g:profiler colons in docs

#330 WackerO closed 2 weeks ago
1
311 add module gsea

#329 thomas-tams opened 4 weeks ago
2
Modify differential/main.nf to include limma

#328 syyang93 closed 3 weeks ago
1
311 add module gsea

#327 thomas-tams closed 4 weeks ago
2
[Dev ratio] add plot exploratory

#326 suzannejin closed 3 weeks ago
1
Mixed-model in Limma

#325 KamilMaliszArdigen opened 4 weeks ago
4
shorten test_experimental into the essential tests

#324 suzannejin closed 4 weeks ago
1
add module GPROFILER2

#323 suzannejin closed 3 weeks ago
0
add module DESEQ2

#322 suzannejin closed 2 weeks ago
2
add test data

#321 suzannejin opened 1 month ago
4
[dev-ratio] update propr container and propd.R

#320 suzannejin closed 1 month ago
1
Incorporation of IHW correction into the pipeline

#319 KamilMaliszArdigen opened 1 month ago
0
move pathway related logic out of differential and correlation subworkflows

#318 bjlang closed 3 weeks ago
1
update rmarkdown notebook

#317 suzannejin opened 1 month ago
0
add plot_differential

#316 suzannejin opened 1 month ago
0
add plot_exploratory

#315 suzannejin opened 1 month ago
0
handle compability between study type and analysis pathway

#314 suzannejin opened 1 month ago
0
better handling of ext.args vs toolsheet args

#313 suzannejin opened 1 month ago
0
better intertalk between params and toolsheet

#312 suzannejin opened 1 month ago
0