Description

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Input

name:type
description
pattern

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

sample_treatment_col:string

The column in the sample sheet that should be used to define groups for comparison

reference:string

The value within the contrast_variable column of the sample sheet that should be used to derive the reference samples

target:string

The value within the contrast_variable column of the sample sheet that should be used to derive the target samples

meta2:map

Groovy map containing study-wide metadata related to the sample sheet and matrix

samplesheet:file

CSV or TSV format sample sheet with sample metadata

counts:file

Raw TSV or CSV format expression matrix

Output

name:type
description
pattern

translated_mrna

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.translated_mRNA.anota2seq.results.tsv:file

anota2seq results for the ‘translated mRNA’ analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.

.translated_mRNA.anota2seq.results.tsv

total_mrna

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.total_mRNA.anota2seq.results.tsv:file

anota2seq results for the ‘translated mRNA’ analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.

.total_mRNA.anota2seq.results.tsv

translation

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.translation.anota2seq.results.tsv:file

anota2seq results for the ‘translated mRNA’ analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.

.translation.anota2seq.results.tsv

buffering

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.buffering.anota2seq.results.tsv:file

anota2seq results for the ‘translated mRNA’ analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.

.buffering.anota2seq.results.tsv

mrna_abundance

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.mRNA_abundance.anota2seq.results.tsv:file

anota2seq results for the ‘mRNA abunance’ analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.

.mRNA_abundance.anota2seq.results.tsv

rdata

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.Anota2seqDataSet.rds:file

Serialised Anota2seqDataSet object

.Anota2seqDataSet.rds

fold_change_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.fold_change.png:file

A fold change plot in PNG format, from anota2seq’s anota2seqPlotFC() method.

.fold_change.png

interaction_p_distribution_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.interaction_p_distribution.pdf:file

The distribution of p-values and adjusted p-values for the omnibus interaction (both using densities and histograms). The second page of the pdf displays the same plots but for the RVM statistics if RVM is used.

.interaction_p_distribution.pdf

residual_distribution_summary_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.residual_distribution_summary.jpeg:file

Summary plot for assessing normal distribution of regression residuals.

.residual_distribution_summary.jpeg

residual_vs_fitted_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.residual_vs_fitted.jpeg:file

QC plot showing residuals against fitted values.

.residual_vs_fitted.jpeg

rvm_fit_for_all_contrasts_group_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.rvm_fit_for_all_contrasts_group.jpg:file

QC plot showing the CDF of variance (theoretical vs empirical), all contrasts.

.rvm_fit_for_all_contrasts_group.jpg

rvm_fit_for_interactions_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.rvm_fit_for_interactions.jpg:file

QC plot showing the CDF of variance (theoretical vs empirical), for interactions.

.rvm_fit_for_interactions.jpg

rvm_fit_for_omnibus_group_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.rvm_fit_for_omnibus_group.jpg:file

QC plot showing the CDF of variance (theoretical vs empirical), for omnibus group.

.rvm_fit_for_omnibus_group.jpg

simulated_vs_obt_dfbetas_without_interaction_plot

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.simulated_vs_obt_dfbetas_without_interaction.pdf:file

Bar graphs of the frequencies of outlier dfbetas using different dfbetas thresholds.

.simulated_vs_obt_dfbetas_without_interaction.pdf

session_info

meta:map

Groovy Map containing contrast information. e.g. [ id:‘contrast1’, blocking:‘patient’ ]

*.R_sessionInfo.log:file

dump of R SessionInfo

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
riboseq
maintainer
Github user pinin4fjords
get in touch
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