Nextflow Modules
Showing module(s) with keyword "cna"
| Module | Keywords | Description |
|---|---|---|
| nf-core/cnvnator/cnvnator | cnvnator cnv cna | CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads. |
| nf-core/cnvnator/convert2vcf | cnvnator cnv cna | convert2vcf.pl is command line tool to convert CNVnator calls to vcf format. |
| nf-core/cnvpytor/importreaddepth | read depth cnv cna call | command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file. |
| nf-core/controlfreec/assesssignificance | cna cnv somatic single tumor-only | Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC |
| nf-core/controlfreec/freec | cna cnv somatic single tumor-only | Copy number and genotype annotation from whole genome and whole exome sequencing data |
| nf-core/controlfreec/freec2bed | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/freec2circos | cna cnv somatic single tumor-only | Format Freec output to circos input format |
| nf-core/controlfreec/makegraph | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/makegraph2 | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/ichorcna/createpon | ichorcna cnv cna cfDNA wgs panel_of_normals | ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals |
| nf-core/ichorcna/run | ichorcna cnv cna cfDNA wgs | ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA |