sitadela

DOI: 10.18129/B9.bioc.sitadela    

This is the development version of sitadela; for the stable release version, see sitadela.

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Bioconductor version: Development (3.14)

Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.

Author: Panagiotis Moulos [aut, cre]

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

Citation (from within R, enter citation("sitadela")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("sitadela")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sitadela")

 

HTML R Script Building a simple annotation database
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, BiomedicalInformatics, ChIPSeq, DataImport, FunctionalGenomics, RNASeq, Sequencing, Software, SystemsBiology, Transcription, Transcriptomics, WorkflowStep
Version 1.1.1
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils
LinkingTo
Suggests BSgenome, knitr, rmarkdown, RMySQL, RUnit
SystemRequirements
Enhances
URL https://github.com/pmoulos/sitadela
BugReports https://github.com/pmoulos/sitadela/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sitadela_1.1.1.tar.gz
Windows Binary sitadela_1.1.1.zip
macOS 10.13 (High Sierra) sitadela_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/sitadela
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sitadela
Package Short Url https://bioconductor.org/packages/sitadela/
Package Downloads Report Download Stats

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