Description

build and deploy Shiny apps for interactively mining differential abundance data

Input

name:type
description
pattern

meta:map

Groovy Map containing information on experiment, at a minimum an id. e.g. [ id:‘test’ ]

sample:file

CSV-format sample sheet with sample metadata

feature_meta:file

TSV-format feature (e.g. gene) metadata

assay_files:file

List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).

meta2:map

Groovy Map containing information on experiment, at a minimum an id. To match meta. e.g. [ id:‘test’ ]

contrasts:file

CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.

differential_results:file

List of TSV-format differential analysis outputs, one per row of the contrasts file

contrast_stats_assay:file

contrast statistics

Output

name:type
description
pattern

app

meta:map

Groovy Map containing information on experiment. e.g. [ id:‘test’ ]

*/data.rds:file

The mini R script required build an application from data.rds.

app/app.R

*/app.R:file

The mini R script required build an application from data.rds.

app/app.R

versions

versions.yml:file

File containing software versions

versions.yml

Tools

shinyngs
AGPL v3

Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.

github.com/pinin4fjords/shinyngs rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs https://github.com/pinin4fjords/shinyngs
differentialabundance
Github user pinin4fjords
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