パッケージ: r-bioc-ensembldb (2.22.0+dfsg-1)

[ ソース: r-bioc-ensembldb  ]

GNU R utilities to create and use an Ensembl based annotation database

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

その他の r-bioc-ensembldb 関連パッケージ

• dep: r-api-4.0

  以下のパッケージによって提供される仮想パッケージです: r-base-core

• dep: r-api-bioc-3.16

  以下のパッケージによって提供される仮想パッケージです: r-bioc-biocgenerics

• dep: r-base-core (>= 4.2.2.20221110-1)

  GNU R core of statistical computation and graphics system

• dep: r-bioc-annotationdbi (>= 1.31.19)

  GNU R Annotation Database Interface for BioConductor

• dep: r-bioc-annotationfilter (>= 1.5.2)

  facilities for filtering Bioconductor annotation resources

• dep: r-bioc-biobase

  base functions for Bioconductor

• dep: r-bioc-biocgenerics (>= 0.15.10)

  generic functions for Bioconductor

• dep: r-bioc-biostrings (>= 2.47.9)

  GNU R string objects representing biological sequences

• dep: r-bioc-genomeinfodb

  BioConductor utilities for manipulating chromosome identifiers

• dep: r-bioc-genomicfeatures (>= 1.49.6)

  GNU R tools for making and manipulating transcript centric annotations

• dep: r-bioc-genomicranges (>= 1.31.18)

  BioConductor representation and manipulation of genomic intervals

• dep: r-bioc-iranges (>= 2.13.24)

  GNU R low-level containers for storing sets of integer ranges

• dep: r-bioc-protgenerics

  S4 generic functions for Bioconductor proteomics infrastructure

• dep: r-bioc-rsamtools

  GNU R binary alignment (BAM), variant call (BCF), or tabix file import

• dep: r-bioc-rtracklayer

  GNU R interface to genome browsers and their annotation tracks

• dep: r-bioc-s4vectors (>= 0.23.10)

  BioConductor S4 implementation of vectors and lists

• dep: r-cran-curl

  GNU R modern and flexible web client for R

• dep: r-cran-dbi

  GNU R package providing a generic database interface

• dep: r-cran-rsqlite (>= 1.1)

  Database Interface R driver for SQLite

• sug: r-bioc-annotationhub

  GNU R client to access AnnotationHub resources

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-bioc-ggbio (>= 1.24.0)

  Visualization tools for genomic data

• sug: r-bioc-gviz (>= 1.20.0)

  Plotting data and annotation information along genomic coordinates

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-magrittr

  GNU R forward-pipe operator

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-testthat

  GNU R testsuite

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