modules/hicexplorer_hicpca

Computes PCA eigenvectors for a Hi-C matrix.

eigenvectorsPCAhicPCA

https://github.com/nf-core/modules/[...]/modules/nf-core/hicexplorer/hicpca

Description

Computes PCA eigenvectors for a Hi-C matrix.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, bin:50000 ]

`matrix`
`:file`

HiCExplorer matrix in h5 format

Output

name:type

description

pattern

`results`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, bin:50000 ]

`${prefix}_*`
`:file`

Outputs of hicPCA

`pca1`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, bin:50000 ]

`${prefix}_pca1.$format`
`:file`

PCA1 file

`pca2`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, bin:50000 ]

`${prefix}_pca2.$format`
`:file`

PCA2 file

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

hicexplorer
GPL v3

Set of programs to process, analyze and visualize Hi-C and capture Hi-C data

hicexplorer.readthedocs.io https://github.com/deeptools/HiCExplorer 10.1038/s41467-017-02525-w

modules/hicexplorer_hicpca

Description

Input

`meta`
`:map`

`matrix`
`:file`

Output

`results`

`meta`
`:map`

`${prefix}_*`
`:file`

`pca1`

`meta`
`:map`

`${prefix}_pca1.$format`
`:file`

`pca2`

`meta`
`:map`

`${prefix}_pca2.$format`
`:file`

`versions`

`versions.yml`
`:file`

Tools

hicexplorer
GPL v3

maintainer

get in touch

modules/hicexplorer_hicpca

Description

Input

meta:map

matrix:file

Output

results

meta:map

${prefix}_*:file

pca1

meta:map

${prefix}_pca1.$format:file

pca2

meta:map

${prefix}_pca2.$format:file

versions

versions.yml:file

Tools

hicexplorer GPL v3

maintainer

get in touch

`meta`
`:map`

`matrix`
`:file`

`results`

`meta`
`:map`

`${prefix}_*`
`:file`

`pca1`

`meta`
`:map`

`${prefix}_pca1.$format`
`:file`

`pca2`

`meta`
`:map`

`${prefix}_pca2.$format`
`:file`

`versions`

`versions.yml`
`:file`

hicexplorer
GPL v3