gread: Fast Reading and Processing of Common Gene Annotation and...

In openanalytics/gread: Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Description

The gread package allows to read and process common gene annotation and next generation sequencing file formats easily. It currently supports:

• Gene Feature Format or gff using rtracklayer package,

• Gene Transfer Format or gtf (also referred to as gff 2.5 at times) using rtracklayer package,

• Browser Extensible Data or bed format using the data.table package.

• Binary sequence Alignment/Map Format or bam format using GenomicAlignments package.

In addition, it also provides additional utility functions such as:

• Filling missing intron coordinates - construct_introns,

• Extracting particular features from gff/gtf files - extract,

• Extract non-overlapping features (e.g., genes, introns) etc. - non_overlaps

References

http://gmod.org/wiki/GFF3
http://www.ensembl.org/info/website/upload/gff.html
https://github.com/rdatatable/data.table
https://bioconductor.org

See Also

read_format read_gff read_gtf read_bed read_bam extract construct_introns

openanalytics/gread documentation built on May 24, 2019, 2:29 p.m.