Description

reads a maxQuant proteinGroups file with Proteus

Input

name:type
description
pattern

meta{:bash}

:map

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

samplesheet{:bash}

:file

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

intensities{:bash}

: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{:bash}

meta{:bash}

:file

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

*dendrogram.png{:bash}

:file

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

mean_var_plot{:bash}

meta{:bash}

:file

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

*mean_variance_relationship.png{:bash}

:file

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

raw_dist_plot{:bash}

meta{:bash}

:file

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

*raw_distributions.png{:bash}

:file

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

norm_dist_plot{:bash}

meta{:bash}

:file

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

*normalized_distributions.png{:bash}

:file

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

raw_rdata{:bash}

meta{:bash}

:file

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

*raw_proteingroups.rds{:bash}

:file

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

norm_rdata{:bash}

meta{:bash}

:file

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

*normalized_proteingroups.rds{:bash}

:file

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

raw_tab{:bash}

meta{:bash}

:file

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

*raw_proteingroups_tab.tsv{:bash}

:file

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

norm_tab{:bash}

meta{:bash}

:file

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

*normalized_proteingroups_tab.tsv{:bash}

:file

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

session_info{:bash}

meta{:bash}

:file

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

*R_sessionInfo.log{:bash}

:file

LOG file of the R sessionInfo from the module run

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
differentialabundance
maintainer
Github user WackerO
get in touch
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