Nextflow Modules
Showing module(s) with keyword "rnaseq"
| Module | Keywords | Description |
|---|---|---|
| nf-core/anota2seq/anota2seqrun | riboseq rnaseq translation differential | Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq |
| nf-core/ctatsplicing/prepgenomelib | splicing cancer rna rnaseq | Reference preparation for CTAT-splicing |
| nf-core/ctatsplicing/startocancerintrons | splicing cancer rna rnaseq | Detection and annotation of aberrant splicing isoforms in cancer transcriptomes |
| nf-core/custom/multiqccustombiotype | biotype featurecounts multiqc rnaseq qc | Generate MultiQC-compatible biotype count summaries from featureCounts output |
| nf-core/dupradar | rnaseq duplication genomics | Assessment of duplication rates in RNA-Seq datasets |
| nf-core/lsa/cosine | similarity cosine clustering rnaseq heatmap | Calculates the cosine similarity matrix between samples based on a gene expression matrix. |
| nf-core/portcullis/full | rnaseq genome splice junction | Run all Portcullis steps in one go |
| nf-core/qualimap/rnaseq | quality control qc rnaseq | Evaluate alignment data |
| nf-core/rnaquast | rna assembly rnaseq de novo quality control | Assess the quality of an RNAseq assembly with or without a reference genome |
| nf-core/rseqc/inferexperiment | rnaseq strandedness experiment | Infer strandedness from sequencing reads |
| nf-core/rseqc/junctionannotation | junctions splicing rnaseq | compare detected splice junctions to reference gene model |
| nf-core/rseqc/junctionsaturation | junctions splicing rnaseq | compare detected splice junctions to reference gene model |
| nf-core/rseqc/readdistribution | read distribution genomics rnaseq | Calculate how mapped reads are distributed over genomic features |
| nf-core/rseqc/readduplication | rnaseq duplication sequence-based mapping-based | Calculate read duplication rate |
| nf-core/rseqc/splitbam | bam split rnaseq quality control | Split BAM file based on gene list in BED format |
| nf-core/rseqc/tin | rnaseq transcript integrity | Calculate TIN (transcript integrity number) from RNA-seq reads |
| nf-core/rustqc | rnaseq quality control qc bam dupradar featurecounts rseqc preseq qualimap samtools | All-in-one RNA-seq post-alignment QC replacing dupRadar, featureCounts biotype QC, RSeQC, Preseq, Qualimap, and SAMtools stats |
| nf-core/shinyngs/staticdifferential | rnaseq plot differential shinyngs | Make plots for interpretation of differential abundance statistics |
| nf-core/variancepartition/dream | rnaseq dream variancepartition | Runs a differential expression analysis with dream() from variancePartition R package |
| nf-core/velocyto | count rnaseq rna velocity bam | Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use `Path(resolve_path=True)` and breaks the nextflow logic of symbolic links. If in the work dir velocyto find a file named EXACTLY `cellsorted_[ORIGINAL_BAM_NAME]` it will skip the samtools sort step. Cellsorted bam file should be cell sorted with: ```bash samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam ``` See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT: ```groovy withName: SAMTOOLS_SORT { ext.prefix = { "cellsorted_${bam.baseName}" } ext.args = '-t CB -O BAM' } ``` Optional mask must be passed with `ext.args` and option `--mask` This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also [velocyto tutorial](https://velocyto.org/velocyto.py/tutorial/cli.html#notes-on-first-runtime-and-parallelization) |