Paket: r-bioc-ensembldb (2.6.5+dfsg-1)

[ Quellcode: 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.

Andere Pakete mit Bezug zu r-bioc-ensembldb

• dep: r-api-3.5

  virtuelles Paket, bereitgestellt durch r-base-core

• dep: r-api-bioc-3.8

  virtuelles Paket, bereitgestellt durch r-bioc-biocgenerics

• dep: r-base-core (>= 3.5.2-1)

  GNU R - System für statistische Berechnungen und Grafik - Kern

• 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 (>= 1.29.10)

  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

  BioConductor S4 implementation of vectors and lists

• dep: r-cran-curl

  Moderner und flexibler Web-Client für GNU R

• dep: r-cran-dbi

  GNU-R-Paket, stellt eine allgemeine Datenbankschnittstelle bereit

• dep: r-cran-rsqlite (>= 1.1)

  R-Datenbank-Schnittstellentreiber für SQLite

• sug: r-bioc-annotationhub

  GNU R client to access AnnotationHub resources

• 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-testthat

  GNU R testsuite

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Architektur	Paketgröße	Größe (installiert)	Dateien
all	1.414,5 kB	2.268,0 kB	[Liste der Dateien]