Nextflow Modules
Showing module(s) with keyword "rnaseq"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/anota2seq/anota2seqrun | Process | riboseq rnaseq translation differential | Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq |
| nf-core/arcane/filter | Process | single-cell rnaseq filter gtf fasta transcriptomics | Filter GTF annotations and genome sequence for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/arcane/index | Process | single-cell rnaseq index kmer hash transcriptomics | Build a k-mer hash index from a filtered reference for alignment-free single-cell RNA-seq quantification with Arcane |
| nf-core/bam_qc_rnaseq | Workflow | rnaseq bam qc quality_control preseq qualimap dupradar rseqc featurecounts biotype | Run post-alignment QC tools on RNA-seq BAM files including library complexity estimation (Preseq), biotype QC (featureCounts), RNA-seq-specific QC metrics (Qualimap), duplicate rate analysis (dupRadar), and comprehensive RSeQC analysis. |
| nf-core/bam_rseqc | Workflow | rnaseq experiment inferexperiment bamstat innerdistance junctionannotation junctionsaturation readdistribution readduplication tin | Subworkflow to run multiple commands in the RSeqC package |
| nf-core/ctatsplicing/prepgenomelib | Process | splicing cancer rna rnaseq | Reference preparation for CTAT-splicing |
| nf-core/ctatsplicing/startocancerintrons | Process | splicing cancer rna rnaseq | Detection and annotation of aberrant splicing isoforms in cancer transcriptomes |
| nf-core/custom/multiqccustombiotype | Process | biotype featurecounts multiqc rnaseq qc | Generate MultiQC-compatible biotype count summaries from featureCounts output |
| nf-core/dotseq/dotseq | Process | riboseq rnaseq translation differential orf | Detect differential ORF usage (DOU) and ORF-level differential translation efficiency (DTE) from Ribo-seq with matched RNA-seq using DOTSeq. Wraps DOTSeqDataSetsFromSummarizeOverlaps() + DOTSeq() + getContrasts() and emits the package's native contrast tables plus plotDOT() visualisations. |
| nf-core/dupradar | Process | rnaseq duplication genomics | Assessment of duplication rates in RNA-Seq datasets |
| nf-core/fastq_align_hisat2 | Workflow | align sort rnaseq genome fastq bam sam cram | Align reads to a reference genome using hisat2 then sort with samtools |
| nf-core/fastq_qc_trim_filter_setstrandedness | Workflow | fastq rnaseq rrna trimming subsample strandedness | Performs linting, quality control, trimming, filtering, and strandedness determination on RNA-seq FASTQ files, preparing them for downstream analysis. |
| nf-core/lsa/cosine | Process | similarity cosine clustering rnaseq heatmap | Calculates the cosine similarity matrix between samples based on a gene expression matrix. |
| nf-core/portcullis/full | Process | rnaseq genome splice junction | Run all Portcullis steps in one go |
| nf-core/qualimap/rnaseq | Process | quality control qc rnaseq | Evaluate alignment data |
| nf-core/quantify_pseudo_alignment | Workflow | rnaseq quantification kallisto salmon |