Nextflow Modules
Showing module(s) with keyword "rsem"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/custom/rsemmergecounts | Process | rsem merge counts gene expression | Merge per-sample RSEM results into wide and long format TSV matrices |
| nf-core/custom/tx2gene | Process | gene gtf pseudoalignment rsem transcript | Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. |
| nf-core/quantify_rsem | Workflow | rnaseq quantification rsem tximport | Perform quantification with RSEM to produce count tables, legacy merge matrices, and SummarizedExperiment objects |
| nf-core/quant_tximport_summarizedexperiment | Workflow | rnaseq quantification tximport summarizedexperiment salmon kallisto rsem | Post-process transcript-level quantification results using tximport to produce count matrices and SummarizedExperiment objects |
| nf-core/rsem/calculateexpression | Process | rsem expression quantification | Calculate expression with RSEM |
| nf-core/rsem/preparereference | Process | rsem genome index | Prepare a reference genome for RSEM |
| nf-core/sentieon/rsemcalculateexpression | Process | rsem expression quantification sentieon | Calculate expression with RSEM |
| nf-core/sentieon/rsempreparereference | Process | rsem genome index sentieon | Prepare a reference genome for RSEM |
| nf-core/tximeta/tximport | Process | gene kallisto pseudoalignment rsem salmon transcript | Import transcript-level abundances and estimated counts for gene-level analysis packages |
| nf-core/umitools/prepareforrsem | Process | umitools rsem salmon dedup | Make the output from umi_tools dedup or group compatible with RSEM |