nf-core/differentialabundance

Issues

• add test data

  #321 opened 2 months ago by suzannejin
  4

• https://nf-co.re/differentialabundance/1.5.0/docs/usage/#g should be the full name:gprofiler2, not just g

  #305 opened a month ago by vmkalbskopf
  1

• Volcano plot in report shows less genes than in 'plots/differential/*/png/volcano.png'

  #340 opened a month ago by d4straub
  10

• Error with `ch_gene_sets` when running gprofiler analysis without gmt file

  #360 opened a month ago by Mathias-Boulanger
  1

• Unable to run pipeline – please provide test data

  #358 opened a month ago by febedtu
  1

• Create subworkflow for deconvolution analyses in bulk data

  #361 opened a month ago by apeltzer
  0

• Assess if we should simplify CUSTOM_TABULARTO GSEACLS

  #355 opened a month ago by nschcolnicov
  2

• Replace unmaintained Proteus with maxLFQ, by author's suggestion.

  #356 opened a month ago by vmkalbskopf
  0

• Error with samplesheet.csv with two column headers that have prefix in common

  #249 opened a month ago by aghr
  16

• Importing Data into Chart Studio Cloud

  #353 opened a month ago by Faitero
  0

• Add module decoupleR to nf-core/modules

  #350 opened a month ago by atrigila
  1

• Add nf-core module PROGENy to nf-core/differentialabundance

  #351 opened a month ago by atrigila
  0

• Test full profile not working in dev

  #347 opened a month ago by nschcolnicov
  1

• Add nf-core module DoRothEA to nf-core/differentialabundance

  #352 opened a month ago by atrigila
  0

• Add module DoRothEA to nf-core/modules

  #349 opened a month ago by atrigila
  0

• Error in TABULAR_TO_GSEA_CHIP

  #258 opened 9 months ago by acpicornell
  4

• Gene name in differential and abundance tables

  #345 opened a month ago by oquendoM
  0

• Missing colour and hover labels in interactive report volcano plot

  #270 opened 7 months ago by ajeffs
  6

• add module DESEQ2

  #322 opened a month ago by suzannejin
  2

• Create 'differential' subworkflow

  #341 opened 2 months ago by pinin4fjords
  1

• Allow lfc_threshold to be a float

  #338 opened 2 months ago by vmkalbskopf
  0

• Mixed-model in Limma

  #325 opened 2 months ago by KamilMaliszArdigen
  4

• add module GPROFILER2

  #323 opened 2 months ago by suzannejin
  0

• update rmarkdown notebook

  #317 opened 2 months ago by suzannejin
  0

• add plot_differential

  #316 opened 2 months ago by suzannejin
  0

• add module LIMMA

  #310 opened 2 months ago by suzannejin
  0

• add module GSEA

  #311 opened 2 months ago by suzannejin
  1

• add plot_exploratory

  #315 opened 2 months ago by suzannejin
  0

• update documentation

  #307 opened 2 months ago by suzannejin
  0

• handle compability between study type and analysis pathway

  #314 opened 2 months ago by suzannejin
  0

• better intertalk between params and toolsheet

  #312 opened 2 months ago by suzannejin
  0

• Incorporation of IHW correction into the pipeline

  #319 opened 2 months ago by KamilMaliszArdigen
  0

• better handling of ext.args vs toolsheet args

  #313 opened 2 months ago by suzannejin
  0

• Restructure the way how the 'experimental' branch is called by main

  #309 opened 2 months ago by suzannejin
  0

• Command error: gtf2featureAnnotation.R: command not found ---pipeline test

  #291 opened 3 months ago by cloud2266
  6

• deseq_lfc_threshold parameter is not working as intended.

  #295 opened 3 months ago by erdikucuk
  0

• Gene sets in the shinyngs app

  #294 opened 3 months ago by Jeff-hard
  0

• volcano plot cannot be edited in the report

  #287 opened 3 months ago by jml96
  3

• How to use `--transcript_length_matrix` with nf-core/rnaseq `--aligner star_rsem` output?

  #279 opened 5 months ago by olgabot
  2

• Provide a parameter to disable rmarkdown report creation in the differential abundance pipeline

  #275 opened 7 months ago by shreya-sharma20
  2

• release differentialabundance

  #251 opened 6 months ago by WackerO
  1

• For spike-in analysis, remove control features from outputs

  #277 opened 7 months ago by dshechter
  0

• Requests: Enhancements to DESeq2 csv outputs and PDF outputs

  #276 opened 7 months ago by dshechter
  0

• Normalized/Raw data mishap on the report

  #271 opened 7 months ago by rekren
  1

• Auto-format sample names

  #262 opened 8 months ago by nick-youngblut
  2

• GSEA html reports have broken links to png and TSV files

  #260 opened 8 months ago by vmkalbskopf
  1

• PosixFileAttributeView

  #263 opened 8 months ago by nick-youngblut
  0

• Failed to publish file => double forward slashes

  #261 opened 8 months ago by nick-youngblut
  0

• Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)` terminated with an error exit status (125)

  #252 opened 9 months ago by dgoswamia
  4

• Please pin the version of the nf-validation plugin!

  #248 opened 9 months ago by mirpedrol
  1