kek12e/gyro

R wrapper scripts for genomic tools

gyro

R wrapper scripts for genomic tools

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Overview

gyro provides a set of wrapper scripts for executing popular command-line genomic tools from R. Gyro currently only supports Linux-based systems because of it's use of shell pipes and redirection. It may also require the shell R is run in to be bash.

Why?

gyro facilitates the use of genomic programs and pipelines on multiple data sets quickly and easily without the need for shell scripting. In general, the output of gyro functions are the names of the files generated by the output of the program being called. This enables the use of quickly passing the output files of one program as the input files for another program. Below is an example of the execution of a chip-seq pipeline with all fastq files in the current working directory (using magrittr pipes and the converge R package).

# define a vector of file names for all fastq files in the current working directory
f <- files("*.fastq")

# define path to genome chrom sizes file
genome <- "/path/to/genome.chrom.sizes"

# go from fastq to genomewide coverage in a single line
f %>% bowtie("/path/to/bowtieindex") %>% samtoolsView(minQual=10) %>% \
bamToBed %>% bedtoolsGenomeCov(genome) %>% bedGraphToBigWig(genome) -> bigWigs

# without magrittr pipes, one can achieve the same thing as follows
sams <- bowtie(f,"/path/to/bowtieindex")
bams <- samtoolsView(sams,minQual=10)
beds <- bamToBed(bams)
bgs  <- bedtoolsGenomeCov(beds,genome)
bws  <- bedGraphToBigWig(bgs,genome)

Installation

Install devtools if not installed already:

install.packages("devtools")

Then install conifur (convenience functions for R), then gyro:

devtools::install_github("dvera/conifur")
devtools::install_github("dvera/gyro")

The following R packages are recommended:

devtools::install_github("dvera/converge")
devtools::install_github("dvera/travis")

A given program must be installed and available in your $PATH in order to use a gyro script that calls the program. A complete list of programs is tabulated below:

program	gyro function name
bcftools call	bcftoolsCall
bcftools filter	bcftoolsFilter
bcftools merge	bcftoolsMerge
bcftools query	bcftoolsQuery
bcftools view	bcftoolsView
bedtools closest	bedtoolsClosest
bedtools coverage	bedtoolsCoverage
bedtools genomecov	bedtoolsGenomeCov
bedtools intersect	bedtoolsIntersect
bedtools makewindows	bedtoolsMakeWindows
bedtools map	bedtoolsMap
bedtools merge	bedtoolsMerge
bedtools multicov	bedtoolsMultiCov
bedtools shuffle	bedtoolsShuffle
bedtools slop	bedtoolsSlop
bedtools subtract	bedtoolsSubtract
bfc	bfc
bgzip	bgzip
bowtie	bowtie
bowtie2	bowtie2
bwa aln	bwaAln
bwa index	bwaIndex
bwa sampe	bwaSampe
bwa samse	bwaSamse
bwa sw	bwaSw
cuffdiff	cuffdiff
cufflinks	cufflinks
cutadapt	cutadapt
FastQC	fastqc
fastqp	fastqp
featureCounts	featureCounts
hisat	hisat
kallisto quant	kallistoQuant
kent utils bedClip	kentBedClip
kent utils bigWigAverageOverBed	kentBigWigAverageOverBed
kent utils liftOver	kentLiftOver
macs callpeak	macsCallPeak
sambamba rmdup	sambambaRmdup
samtools cat	samtoolsCat
samtools index	samtoolsIndex
samtools merge	samtoolsMerge
samtools mpileup	samtoolsMpileup
samtools sort	samtoolsSort
samtools view	samtoolsView
seqtk seq	seqtkSeq
seqtk trimfq	seqtkTrimfq
stringtie	stringtie
tophat	tophat