nf-core / differentialabundance

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

https://nf-co.re/differentialabundance

nf-core/differentialabundance Issues

Name of blocking variable not correctly recognized
Updated 3 months ago3
Continuous covariates
Updated 3 months ago1
release differentialabundance
Updated 3 months ago
Error with samplesheet.csv with two column headers that have prefix in common
Updated 3 months ago
Bad job name on LSF (too long, special chars?)
Closed 8 months ago3
Please pin the version of the nf-validation plugin!
Updated 3 months ago
Differential expression at transcript level
Updated 3 months ago5
Proteomics pipeline does not create the required file for the explotarory plot
Closed 3 months ago4
Mark --matrix as a required parameter in the parameter section on the diffabundance website
Updated 3 months ago1
Plotting of data where the p-value is zero
Closed 3 months ago2
DiffAbundance v1.4.0 does not work with most recent nextflow 23.10.1.5891
Closed 3 months ago3
GSEA_GSEA error:: Missing output file(s) `*butterfly_plot.png`?
Closed 3 months ago6
Dev version: On parameters website list parameter gene_sets_files in section GSEA
Updated 3 months ago
URGENT: pin nf-validation version
Closed 4 months ago2
Remove parameter --gsea_run
Updated 4 months ago
Setting differential_subset_to_contrast_samples: true with output from nfcore rnaseq causes error
Updated 4 months ago
RMARKDOWNNOTEBOOK - Error in \`cor()\`: ! supply both 'x' and 'y' or a matrix-like 'x'
Updated 4 months ago1
Command error: .command.sh: line 3: gtf2featureAnnotation.R: command not found
Closed 5 months ago1
Add log2_assays docu to nextflow_schema after shiny fix
Updated 5 months ago3
"exclude" samples aren't respected in SHINYNGS_STATICEXPLORATORY - Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x'
Updated 5 months ago5
incomplete matches of variable name
Closed 5 months ago1
technical replicates
Updated 5 months ago3
Simplify pipeline parameters
Updated 5 months ago3
pandoc conversion failed in differential abundance test run
Closed 5 months ago2
PLOT_EXPLORATORY module breaks with large number of samples.
Updated 5 months ago1
Add gprofiler2 functionality
Closed 6 months ago1
Errors thrown out in NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL
Closed 6 months ago3
Final report, volcano plot: points wrongly marked red
Closed 6 months ago1
Null device 1 OR error in nsub parameter
Closed 6 months ago4
Multiple variables/interactions
Updated 6 months ago1
Getting "Error in data[[rowvar]] : attempt to select less than one element in get1index" when using transcript_counts from rnaseq pipeline
Closed 7 months ago2
Switching to rlog for deseq2 vs method truncates pipeline output
Closed 7 months ago4
Sample metadata table in the html report is not paginating
Closed 7 months ago
Documentation does not fit pipeline behaviour.
Closed 8 months ago3
Output a parameter-resolved R Markdown document, as well as rendered HTML
Closed 8 months ago
workaround OPENBLAS using all cores problem
Closed 8 months ago1
Update subway map
Closed 8 months ago
Document sample sheet for Affy arrays
Closed 8 months ago
input samplesheet template for affimetrix data
Closed 8 months ago5
Proxy-Setting/Prevent R from Internet Search
Closed 8 months ago4
add apeglm log fold change shrinkage
Updated 8 months ago2
Error with DESEQ2_DIFFERENTIAL when using spike-in controls: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Closed 8 months ago
Sample exclusion options fail due to contrast-wise normalisation
Closed 8 months ago
Add link to example Shiny app
Closed 8 months ago1
Duplicated "using" word
Closed 8 months ago
Error about r-shinyngs:1.7.1--r42hdfd78af_1 when used nf-core download with singularity
Closed 8 months ago3
Error about r-shinyngs:1.7.1--r42hdfd78af_1 when used nf-core download with singularity
Closed a year ago
[Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv
Closed a year ago
Download fails with singularity errors
Closed a year ago
Skip outlier detection with low replication
Closed a year ago