HajkD / seqreadr

Read Genomic File Formats with R

seqreadr

Read Biological Sequences File Formats with R.

Motivation:

Several (standardized) file formats have been published and are actively used to store, exchange, and analyze biological sequences. The seqreadr package aims to provide read/write functions to work with this variety of sequence file formats.

To avoid re-inventing the wheel the seqreadr package relies on existing interface functions implemented in a variety of R packages. However, additional functionality for sequence quality control is provided by the functions implemented in seqreadr. Furthermore, seqreadr aims to provide a complete collection of sequence file formats and is based on a unifying terminology and nomenclature to avoid learning different package styles etc.

Tutorials

Use Cases for each Sequence File Format:

• FastA/FastQ
• SAM/BAM
• GFF/GTF
• BED/Big Bed
• PSL
• Pairwise Interaction File Format
• Variation File Format
• WIG File Format

NEWS

The current status of the package as well as a detailed history of the functionality of each version of seqreadr can be found in the NEWS section.

Installation

# install developer version of seqreadr
library(devtools)
install_github("HajkD/seqreadr", build_vignettes = TRUE, dependencies = TRUE)

Discussions and Bug Reports

I would be very happy to learn more about potential improvements of the concepts and functions provided in this package.

Furthermore, in case you find some bugs or need additional (more flexible) functionality of parts of this package, please let me know:

https://github.com/HajkD/seqreadr/issues

Based on the following packages

• Biostrings
• refGenome
• GenomicRanges

Input functions implemented in seqreadr

FastA/FastQ File Formats

• read.genome(): Read the genome of a given organism (DNA)
• read.proteome(): Read the proteome of a given organism (Protein)
• read.cds(): Read the CDS of a given organism (DNA)

GFF/GTF File Formats

• read.gtf(): Read GTF (General Transfer Format) Files
• write.gtf(): Write GTF files to hard drive

BED File Formats

• read.bed(): Read BED files
• write.bed(): Write BED files to hard drive