Package: r-bioc-megadepth (1.12.0+ds-2)

[ Source: r-bioc-megadepth  ]

BioCOnductor BigWig and BAM related utilities

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

Other Packages Related to r-bioc-megadepth

• dep: megadepth

  computes coverage from BigWig and BAM sequencing files

• dep: r-api-4.0

  virtual package provided by r-base-core

• dep: r-api-bioc-3.18

  virtual package provided by r-bioc-biocgenerics

• dep: r-bioc-genomicranges

  BioConductor representation and manipulation of genomic intervals

• dep: r-cran-cmdfun

  GNI R framework for building interfaces to shell commands

• dep: r-cran-dplyr

  GNU R grammar of data manipulation

• dep: r-cran-fs

  GNU R cross-platform file system operations

• dep: r-cran-magrittr

  GNU R forward-pipe operator

• dep: r-cran-readr

  GNU R package to read rectangular text data

• dep: r-cran-xfun

  miscellaneous GNU R functions by 'Yihui Xie'

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-bioc-genomeinfodb

  BioConductor utilities for manipulating chromosome identifiers

• sug: r-bioc-rtracklayer

  GNU R interface to genome browsers and their annotation tracks

• sug: r-cran-covr

  test coverage for GNU R packages

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-sessioninfo

  R Session Information

• sug: r-cran-testthat

  GNU R testsuite

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