Nextflow Modules
Showing module(s) with keyword "expression"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/abundance_differential_filter | Workflow | differential abundance expression count matrix fold-change | A subworkflow for filtering differential abundance results |
| nf-core/affy/justrma | Process | affy microarray expression matrix | Read CEL files into an ExpressionSet and generate a matrix |
| nf-core/deseq2/differential | Process | differential expression rna-seq deseq2 | runs a differential expression analysis with DESeq2 |
| nf-core/edger/differential | Process | differential expression rna-seq counts edger | Runs a differential expression analysis on count data with edgeR. Options are passed via `ext.args` as `--option value` pairs: `gene_id_col` (default `gene_id`), `sample_id_col` (`experiment_accession`), `blocking_variables` (`;`-separated sample sheet columns, not combinable with a formula), `subset_to_contrast_samples` (`FALSE`, needs a contrast variable), `exclude_samples_col` and `exclude_samples_values` (`;`-separated), `filter_by_expr` (`FALSE`), `min_count` (`10`), `norm_method` (`TMM`), `test_method` (`qlf` for glmQLFit/glmQLFTest or `lrt` for glmFit/glmLRT), `robust` (`TRUE`), `prior_count` (`2`), `adjust_method` (`BH`) and `round_digits` (no rounding). Defaults that differ from edgeR's own: `robust` is `TRUE` for both `estimateDisp` and `glmQLFit` (edgeR default `FALSE`), and `filterByExpr` is off by default because pipelines usually filter upstream; when enabled, `min_count` is passed as `min.count`. Sample sheet column names, including those used in a formula, are converted with `make.names()`. |
| nf-core/geofetch | Process | GEO expression microarray sequencing | geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA |
| nf-core/geoquery/getgeo | Process | geo expression microarray | Retrieves GEO data from the Gene Expression Omnibus (GEO) |
| nf-core/limma/differential | Process | differential expression microarray limma | runs a differential expression analysis with Limma |
| nf-core/propr/propd | Process | differential proportionality logratio expression propr propd | Perform differential proportionality analysis |
| nf-core/rsem/calculateexpression | Process | rsem expression quantification | Calculate expression with RSEM |
| nf-core/sentieon/rsemcalculateexpression | Process | rsem expression quantification sentieon | Calculate expression with RSEM |
| nf-core/shinyngs/app | Process | differential expression rna-seq deseq2 | build and deploy Shiny apps for interactively mining differential abundance data |
| nf-core/shinyngs/validatefomcomponents | Process | expression features observations validation | validate consistency of feature and sample annotations with matrices and contrasts |