recipe bioconductor-epihet

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/epihet.html

License:

Artistic-2.0

Recipe:

/bioconductor-epihet/meta.yaml

epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis.

package bioconductor-epihet

Versions:

1.13.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

Depends:

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-qvalue >=2.30.0,<2.31.0

• bioconductor-reactomepa >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-doparallel

• r-entropyexplorer

• r-foreach

• r-ggplot2

• r-igraph

• r-pheatmap

• r-rtsne

• r-wgcna

Required By:

Installation

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

conda install bioconductor-epihet

and update with:

conda update bioconductor-epihet

or use the docker container:

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

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

Download stats

Link to this page

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