Nextflow Modules
Showing module(s) with keyword "RNA-seq"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/cellbender/removebackground | Process | cellbender single-cell RNA-seq ambient RNA empty droplets artifact removal | Removes ambient RNA and empty droplet artifacts from single-cell RNA-seq data using CellBender, producing a per-sample output directory with filtered count matrices. |
| cellgeni/cellbender/removebackground_v02 | Process | cellbender cellbender-0.2 single-cell RNA-seq ambient RNA empty droplets artifact removal | Removes ambient RNA and empty droplet artifacts from single-cell RNA-seq data using CellBender 0.2 (0.2.2), producing a per-sample output directory with filtered count matrices. |
| cellgeni/cellbender/removebackground_v03 | Process | cellbender cellbender-0.3 single-cell RNA-seq ambient RNA empty droplets artifact removal | Removes ambient RNA and empty droplet artifacts from single-cell RNA-seq data using CellBender 0.3 (0.3.2), producing a per-sample output directory with filtered count matrices. |
| cellgeni/cellranger/count | Process | cellranger 10x single-cell RNA-seq count matrix | Runs Cell Ranger count on 10x single-cell RNA-seq FASTQs to align reads, generate feature-barcode matrices, and produce per-sample output directories. |
| cellgeni/starsolo10x | Process | STARsolo STAR alignment single-cell 10x RNA-seq count matrix | Aligns 10x single-cell RNA-seq FASTQs to a reference genome using STARsolo, producing per-sample output directories with count matrices and summary statistics. |
| cellgeni/starsoloqc | Process | STARsolo STAR QC quality control single-cell 10x RNA-seq | Collects QC statistics from STARsolo output directories, producing a merged TSV summary of alignment and cell-calling metrics across all samples in a dataset. |
| nf-core/arcashla/extract | Process | HLA genotype RNA-seq | Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates. |
| nf-core/fusioninspector | Process | fusioninspector fusion RNA-seq fastq | Validation of Fusion Transcript Predictions |
| nf-core/fusionreport/detect | Process | sort RNA-seq fusion report detect | fusionreport_detect |
| nf-core/fusionreport/download | Process | sort RNA-seq fusion_report download | Build DB for fusionreport |
| nf-core/immunedeconv | Process | Immune Deconvolution RNA-seq Bioinformatics Tools Computational Immunology | Perform immune cell deconvolution using RNA-seq data and various computational methods. |
| nf-core/leafcutter/clusterregtools | Process | splicing RNA-seq clustering junctions | Cluster RNA-seq junction reads extracted by regtools and refine them based on read counts and ratios for alternative splicing analysis |
| nf-core/leafcutter/differentialsplicing | Process | alternative splicing differential splicing RNA-seq intron usage | Perform differential splicing analysis to identify junctions with significant changes in splicing between conditions |
| nf-core/regtools/junctionsextract | Process | regtools leafcutter RNA-seq splicing | Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format. |