modules/idr

Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible Discovery Rate)

IDRpeaksChIP-seqATAC-seq

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

Description

Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible Discovery Rate)

Input

name:type

description

pattern

`peaks:list`

BED, narrowPeak or broadPeak files of replicates

*

`peak_type:string`

Type of peak file

{narrowPeak,broadPeak,bed}

`prefix:string`

Prefix for output files

Output

name:type

description

pattern

`idr`

`*idrValues.txt:file`

Text file containing IDR values

*.{txt}

`log`

`*log.txt:file`

Log file

*.{txt}

`png`

`*.png:file`

Plot generated by idr

*{.png}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

idr
GPL v2

The IDR (Irreproducible Discovery Rate) framework is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provide highly stable thresholds based on reproducibility.

https://github.com/kundajelab/idr

modules/idr

Description

Input

peaks:list

peak_type:string

prefix:string