Package Recipe 'bioconductor-chromscape'

recipe bioconductor-chromscape

Analysis of single-cell epigenomics datasets with a Shiny App

Homepage:: https://bioconductor.org/packages/3.20/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:

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0,

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.4.0-2, 1.4.0-1, 1.4.0-0, 1.2.0-0, 1.0.0-2, 1.0.0-1

Depends:

on bioconductor-batchelor >=1.26.0,<1.27.0
on bioconductor-batchelor >=1.26.0,<1.27.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-consensusclusterplus >=1.74.0,<1.75.0
on bioconductor-consensusclusterplus >=1.74.0,<1.75.0a0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-delayedarray >=0.36.0,<0.37.0a0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-edger >=4.8.2,<4.9.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scater >=1.38.0,<1.39.0a0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0a0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-colorramps
on r-colourpicker
on r-coop
on r-dplyr
on r-dt
on r-forcats
on r-fs
on r-gggenes
on r-ggplot2
on r-ggrepel
on r-gridextra
on r-irlba
on r-jsonlite
on r-kableextra
on r-matrix
on r-matrixtests
on r-msigdbr
on r-plotly
on r-qs
on r-qualv
on r-rcpp
on r-rlist
on r-rtsne
on r-shiny
on r-shinycssloaders
on r-shinydashboard
on r-shinydashboardplus
on r-shinyfiles
on r-shinyhelper
on r-shinyjs
on r-shinywidgets
on r-stringdist
on r-stringr
on r-tibble
on r-tidyr
on r-umap
on r-viridis

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-chromscape

to add into an existing workspace instead, run:

pixi add bioconductor-chromscape

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-chromscape

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-chromscape

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)