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: Release (3.19)

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 "4.4") and enter:


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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, BiomedicalInformatics, ChIPSeq, DataImport, FunctionalGenomics, RNASeq, Sequencing, Software, SystemsBiology, Transcription, Transcriptomics, WorkflowStep
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
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, txdbmaker, utils
System Requirements
URL	https://github.com/pmoulos/sitadela
Bug Reports	https://github.com/pmoulos/sitadela/issues

Suggests	BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	sitadela_1.12.0.tar.gz
Windows Binary (x86_64)	sitadela_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	sitadela_1.12.0.tgz
macOS Binary (arm64)	sitadela_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sitadela
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sitadela
Bioc Package Browser	https://code.bioconductor.org/browse/sitadela/
Package Short Url	https://bioconductor.org/packages/sitadela/
Package Downloads Report	Download Stats