Pakiet: r-bioc-genomicfeatures (1.34.3+dfsg-1)

[ Pakiet źródłowy: r-bioc-genomicfeatures  ]

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.

Inne pakiety związane z r-bioc-genomicfeatures

• dep: r-api-3.5

  pakiet wirtualny udostępniany przez r-base-core

• dep: r-api-bioc-3.8

  pakiet wirtualny udostępniany przez r-bioc-biocgenerics

• dep: r-base-core (>= 3.5.2-1)

  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-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 (>= 1.15.4)

  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 (>= 1.39.7)

  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-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-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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