README.md

In wanjauk/TxDb.TbruceiTREU927.tritryp43.genes: Annotation package for TxDb object(s)

TxDb.TbruceiTREU927.tritryp43.genes

Transcript annotation package for Trypanosoma brucei brucei TREU927, based on annotated genes from TriTrypDB 43.

This package was generated using the tools from eupathdb-organismdb repository.

Installation

You can install the latest version from Github using:

library('devtools')
install_github('wanjauk/TxDb.TbruceiTREU927.tritryp43.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.TbruceiTREU927.tritryp43.genes)

# list available fields to query
columns(TxDb.TbruceiTREU927.tritryp43.genes)

# get first 10 genes
gene_ids = head(keys(TxDb.TbruceiTREU927.tritryp43.genes), 10)

# gene coordinates and strand
genes = AnnotationDbi::select(TxDb.TbruceiTREU927.tritryp43.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

wanjauk/TxDb.TbruceiTREU927.tritryp43.genes documentation built on Jan. 1, 2021, 12:44 p.m.