recipe r-bulkanalyser

Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.

Homepage:

https://github.com/Core-Bioinformatics/bulkAnalyseR

License:

GPL2 / GPL-2.0-only

Recipe:

/r-bulkanalyser/meta.yaml

package r-bulkanalyser

Versions:

1.1.0-1,  1.1.0-0,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-complexheatmap

• bioconductor-deseq2

• bioconductor-edger

• bioconductor-genie3

• bioconductor-preprocesscore

• r-base >=4.2,<4.3.0a0

• r-circlize

• r-dplyr

• r-dt

• r-ggforce

• r-ggnewscale

• r-ggplot2

• r-ggrastr

• r-ggrepel

• r-ggvenndiagram

• r-glue

• r-gprofiler2

• r-magrittr

• r-matrixstats

• r-noisyr

• r-rcolorbrewer

• r-rlang

• r-scales

• r-shiny

• r-shinyjqui

• r-shinyjs

• r-shinylp

• r-shinywidgets

• r-stringr

• r-tibble

• r-tidyr

• r-upsetr

• r-visnetwork

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install r-bulkanalyser

and update with:

conda update r-bulkanalyser

or use the docker container:

docker pull quay.io/biocontainers/r-bulkanalyser:<tag>

(see r-bulkanalyser/tags for valid values for <tag>)

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Link to this page

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