recipe bioconductor-chromscape

Analysis of single-cell epigenomics datasets with a Shiny App

Homepage

https://bioconductor.org/packages/3.14/bioc/html/ChromSCape.html

License

GPL-3

Recipe

/bioconductor-chromscape/meta.yaml

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, …) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

package bioconductor-chromscape

Versions

1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

Depends

• bioconductor-batchelor >=1.10.0,<1.11.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-consensusclusterplus >=1.58.0,<1.59.0

• bioconductor-delayedarray >=0.20.0,<0.21.0

• bioconductor-edger >=3.36.0,<3.37.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-scater >=1.22.0,<1.23.0

• bioconductor-scran >=1.22.0,<1.23.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-sushi >=1.31.0,<1.32.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• r-base >=4.1,<4.2.0a0

• r-colorramps

• r-colourpicker

• r-coop

• r-dplyr

• r-dt

• r-forcats

• r-fs

• r-ggplot2

• r-irlba

• r-jsonlite

• r-kableextra

• r-matrix

• r-matrixtests

• r-msigdbr

• r-plotly

• r-qs

• r-qualv

• r-rcpp

• r-rlist

• r-rtsne

• r-shiny

• r-shinycssloaders

• r-shinydashboard

• r-shinydashboardplus

• r-shinyfiles

• r-shinyhelper

• r-shinyjs

• r-shinywidgets

• r-stringdist

• r-tibble

• r-tidyr

• r-umap

• r-viridis

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-chromscape

and update with:

conda update bioconductor-chromscape

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-chromscape:<tag>

(see bioconductor-chromscape/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-chromscape/README.html)