TxDb.LmajorFriedlin.tritryp32.genes

Transcript annotation package for Leishmania major strain Friedlin, based on annotated genes from TriTrypDB 32.

This package was generated using the tools from https://github.com/elsayed-lab/eupathdb-organismdb.

Installation

You can install the latest version from Github using:

library('devtools')
install_github('elsayed-lab/TxDb.LmajorFriedlin.tritryp32.genes')

Usage

This package is based on the Bioconductor AnnotationDbi interface. As such, the methods for interacting with this package are similar to the ways one can interact with other commonly-used annotation packages such as TxDb.Hsapiens.UCSC.hg19.knownGene.

Example usage:

library(TxDb.LmajorFriedlin.tritryp32.genes)

# list available fields to query
columns(TxDb.LmajorFriedlin.tritryp32.genes)

# get first 10 genes
gene_ids = head(keys(TxDb.LmajorFriedlin.tritryp32.genes), 10)

# gene coordinates and strand
genes = AnnotationDbi::select(TxDb.LmajorFriedlin.tritryp32.genes, 
                              keys=gene_ids, 
                              keytype='GENEID', 
                              columns=c('TXSTART', 'TXEND', 'TXSTRAND'))

head(genes)

For more information, check out the AnnotationDbi - Introduction to Annotation packages vignette.

Additional resources that may be helpful:

1. http://www.bioconductor.org/help/workflows/annotation-data/
2. http://www.bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html
3. http://training.bioinformatics.ucdavis.edu/docs/2012/05/DAV/lectures/annotation/annotation.html