Nextflow Modules
Showing module(s) with keyword "rna-seq"
| Module | Keywords | Description |
|---|---|---|
| nf-core/deseq2/differential | differential expression rna-seq deseq2 | runs a differential expression analysis with DESeq2 |
| nf-core/disambiguate | disambiguation xenograft explant rna-seq alignment bam | Disambiguates reads aligned to two different organisms (e.g. human and mouse) from the same source of FASTQ files. Useful in explant RNA/DNA-Seq workflows where reads from two species are present. For reads aligned to both organisms, the algorithm compares alignment quality scores to determine the most likely species of origin. Produces four BAM files (uniquely assigned to species A or B, ambiguous for species A or B) and a summary file. |
| nf-core/seq2hla | hla typing rna-seq genomics immunogenetics | Precision HLA typing and expression from RNA-seq data using seq2HLA |
| nf-core/shinyngs/app | differential expression rna-seq deseq2 | build and deploy Shiny apps for interactively mining differential abundance data |
| nf-core/slamdunk/all | slamseq rna-seq mapping snp quantification | Complete SLAMseq analysis pipeline including read mapping, filtering, SNP calling, and quantification |
| nf-core/slamdunk/map | slamseq rna-seq mapping | Slamdunk read mapping using NextGenMap’s SLAMSeq alignment settings. |