modules/shinyngs_app

build and deploy Shiny apps for interactively mining differential abundance data

differentialexpressionrna-seqdeseq2

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

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_shinyngs`

`${task.process}`
`:string`

The name of the process

`shinyngs`
`:string`

The name of the tool

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`shinyngs`
`:string`

The name of the tool

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

The expression to obtain the version of the tool

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

modules/shinyngs_app

Description

Input

`meta`
`:map`

`sample`
`:file`

`feature_meta`
`:file`

`assay_files`
`:file`

`meta2`
`:map`

`contrasts`
`:file`

`differential_results`
`:file`

`contrast_stats_assay`
`:file`

Output

`app`

`meta`
`:map`

`*/data.rds`
`:file`

`*/app.R`
`:file`

`versions_shinyngs`

`${task.process}`
`:string`

`shinyngs`
`:string`

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`shinyngs`
`:string`

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

Tools

shinyngs
AGPL v3

included in

maintainer

get in touch

modules/shinyngs_app

Description

Input

meta:map

sample:file

feature_meta:file

assay_files:file

meta2:map

contrasts:file

differential_results:file

contrast_stats_assay:file

Output

app

meta:map

*/data.rds:file

*/app.R:file

versions_shinyngs

${task.process}:string

shinyngs:string

Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))":eval

Topics

versions

${task.process}:string

shinyngs:string

Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))":eval

Tools

shinyngs AGPL v3

included in

maintainer

get in touch

`meta`
`:map`

`sample`
`:file`

`feature_meta`
`:file`

`assay_files`
`:file`

`meta2`
`:map`

`contrasts`
`:file`

`differential_results`
`:file`

`contrast_stats_assay`
`:file`

`app`

`meta`
`:map`

`*/data.rds`
`:file`

`*/app.R`
`:file`

`versions_shinyngs`

`${task.process}`
`:string`

`shinyngs`
`:string`

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

`versions`

`${task.process}`
`:string`

`shinyngs`
`:string`

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

shinyngs
AGPL v3