modules/proteus_readproteingroups

reads a maxQuant proteinGroups file with Proteus

proteomicsproteusreadproteingroups

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

Description

reads a maxQuant proteinGroups file with Proteus

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:‘’ ]

`samplesheet`
`:file`

CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html

`intensities`
`:file`

proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html

Output

name:type

description

pattern

`dendro_plot`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*dendrogram.png`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`mean_var_plot`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*mean_variance_relationship.png`
`:file`

PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples

`raw_dist_plot`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*raw_distributions.png`
`:file`

PNG file; plot of the intensity/ratio distributions of the raw samples

`norm_dist_plot`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*normalized_distributions.png`
`:file`

PNG file; plot of the intensity/ratio distributions of the normalized samples

`raw_rdata`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*raw_proteingroups.rds`
`:file`

RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info

`norm_rdata`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*normalized_proteingroups.rds`
`:file`

RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info

`raw_tab`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*raw_proteingroups_tab.tsv`
`:file`

TSV-format intensities table from Proteus, contains raw protein intensities

`norm_tab`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*normalized_proteingroups_tab.tsv`
`:file`

TSV-format intensities table from Proteus, contains normalized protein intensities

`session_info`

`meta`
`:file`

PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

`*R_sessionInfo.log`
`:file`

LOG file of the R sessionInfo from the module run

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Topics

name:type

description

pattern

`versions`

`versions.yml`
`:string`

The name of the process

Tools

proteus
GPL v2

R package for analysing proteomics data

github.com/bartongroup/Proteus rdrr.io/github/bartongroup/Proteus https://github.com/bartongroup/Proteus 10.1101/416511