Tag: Athaliana
TAIR Gene Symbols
Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…
Bioconductor – GenomicRanges (development version)
This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…
Bioconductor – TxDb.Athaliana.BioMart.plantsmart51 (development version)
DOI: 10.18129/B9.bioc.TxDb.Athaliana.BioMart.plantsmart51 This is the development version of TxDb.Athaliana.BioMart.plantsmart51; for the stable release version, see TxDb.Athaliana.BioMart.plantsmart51. Annotation package for TxDb object(s) Bioconductor version: Development (3.17) Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart…
Bioconductor – BSgenome
Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…
