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Paketti: r-bioc-genomicfeatures (1.46.4+dfsg-1)

GNU R tools for making and manipulating transcript centric annotations

A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

Muut pakettiin r-bioc-genomicfeatures liittyvät paketit

  • depends
  • recommends
  • suggests
  • dep: r-api-4.0
    näennäispaketti, jonka toteuttaa r-base-core
  • dep: r-api-bioc-3.14
    näennäispaketti, jonka toteuttaa r-bioc-biocgenerics
  • dep: r-base-core (>= 4.1.2-1ubuntu1)
    GNU R core of statistical computation and graphics system
  • dep: r-bioc-annotationdbi (>= 1.41.4)
    GNU R Annotation Database Interface for BioConductor
  • dep: r-bioc-biobase (>= 2.15.1)
    base functions for Bioconductor
  • dep: r-bioc-biocgenerics (>= 0.1.0)
    generic functions for Bioconductor
  • dep: r-bioc-biocio
    standard input and output for Bioconductor packages
  • dep: r-bioc-biomart (>= 2.17.1)
    GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
  • dep: r-bioc-biostrings (>= 2.47.6)
    GNU R string objects representing biological sequences
  • dep: r-bioc-genomeinfodb (>= 1.25.7)
    BioConductor utilities for manipulating chromosome identifiers
  • dep: r-bioc-genomicranges (>= 1.31.17)
    BioConductor representation and manipulation of genomic intervals
  • dep: r-bioc-iranges (>= 2.13.23)
    GNU R low-level containers for storing sets of integer ranges
  • dep: r-bioc-rtracklayer (>= 1.51.5)
    GNU R interface to genome browsers and their annotation tracks
  • dep: r-bioc-s4vectors (>= 0.17.29)
    BioConductor S4 implementation of vectors and lists
  • dep: r-bioc-xvector (>= 0.19.7)
    BioConductor representation and manpulation of external sequences
  • dep: r-cran-dbi
    GNU R package providing a generic database interface
  • dep: r-cran-rcurl
    GNU R General network (HTTP/FTP/...) client interface
  • dep: r-cran-rsqlite (>= 2.0)
    Database Interface R driver for SQLite
  • sug: r-bioc-biocstyle
    standard styles for vignettes and other Bioconductor documents
  • sug: r-bioc-bsgenome
    BioConductor infrastructure for Biostrings-based genome data packages
  • sug: r-bioc-ensembldb
    GNU R utilities to create and use an Ensembl based annotation database
  • sug: r-bioc-genomicalignments (>= 1.15.7)
    BioConductor representation and manipulation of short genomic alignments
  • sug: r-bioc-org.hs.eg.db
    genome-wide annotation for Human
  • sug: r-bioc-rsamtools
    GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  • sug: r-cran-knitr
    GNU R package for dynamic report generation using Literate Programming
  • sug: r-cran-runit
    GNU R package providing unit testing framework

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