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 (3.20)
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("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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, BiomedicalInformatics, ChIPSeq, DataImport, FunctionalGenomics, RNASeq, Sequencing, Software, SystemsBiology, Transcription, Transcriptomics, WorkflowStep |
| Version | 1.14.0 |
| 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 |
See More
| 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | sitadela_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | sitadela_1.14.0.tgz |
| macOS Binary (arm64) | sitadela_1.14.0.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 |