travis is a suite of tools to process, analyze, and visualize bed and bedGraph data in R. Most of travis's functions can be categorized as either operating on beds or on bedGraphs.
Functions that operate on bed files:
- bedBreadth
calculates the total number of bases covered in a bed file
- bedCat
concatenates multiple bed files into one
- bedCenters
takes a bed file and outputs a bed file of the midpoints of the intervals
- bedDivideMeta
divides bed intervals (and optionally surrounding region) into an equal number of windows per interval, regardless of size
- bedDivide
divides equally-sized bed invervals into an equal number of windows per interval
- bedEnds
takes a bed file and outputs a bed file of the ends of the intervals
- bedHist
plots a histogram of interval sizes
- bedOverhangs
calculates frequencies of pairwise distances between the ends of intervals in a single bed file
- bedOverlap
calculates overlap among two sets of bed files
- bedParseLengths
parses bed intervals into separate files based on interval sizes
- bedParseStrands
prases bed intervals into separate files based on strand
- bedPoissonTest
perform a poisson test of interval counts between two bed files with a given set of windows
- bedRecenter
alter the coordinates of a bed file
- bedRemoveChrom
remove intervals on a specific chromosome
- bedSample
randomly sample intevals of a bed file
- bedSizes
load into R sizes of bed intervals
- bedSort
sort a bed file by chromosome/coordinate
- bedStructures
break up a bed12 file into separate components
- bedWords
calculate nucleotide word frequencies for intervals in a bed file
Functions that operate on bedGraph files:
- bgAcf
calculates autocorrelations of bedGraph files
- bgCorMatrix
generates a matrix of pairwise correlations among a set of bedGraph files
- bgHist
plots a histogram of bedGraph scores
- bgIqrNorm
normalizes bedGraphs to have a specified interquartile range
- bgIqr
calculate interquartile ranges of bedGraph files
- bgKsTest
performs a KS test between two bedGraph files
- bgLoess
loess smooths a bedGraph files
- bgOps
perform various operations on single bedGraph files (e.g. transformations) or multiple bedGraph files (averages, differences, variance, ratios)
- bgParseScores
parses bedGraph intervals into multiple bedGraphs based on score
- bgPlot
plot bedGraph scores of specified intervals
- bgPoissonTest
perform a poisson test between two bedGraph files
- bgQuantileNorm
normalizes bedGraphs with quantile normalization
- bgQuantiles
calculates specified quantiles of bedGraph files
- bgRead
reads bedGraph files into R
- bgScatterGrid
calculate a grid of pairwise density scatter plots using a set of bedGraph files
- bgScores
read bedGraph scores into R
- bgSort
sort bedGraph files by score
- bgThreshold
outputs bedGraphs containing intervals exceeding a specified score
- bgUnify
make multiple bedGraph files share an identical set of intervals
- bgZtest
perform a Z-test between two bedGraph files
There are several functions that use bam or sam files:
- bamCount
counts the number of reads in bam files
- bamParseLengths
parses paired-end reads into multiple files based on insert size
- samStats
calcaultes and plots summary statistics for alignment data in sam files
Finally, there are three plotting functions that operate directly on R objects:
- intervalBox
draws a boxplot of data that is binned based on its score in another dimension
- rageHist
plots overlayed histograms of data organized in lists or data frames
- scatterdens
generates a density plot of points in a scatter plot, useful for generating a scatter plot of many points
travis heavily depends on bedtools. Other programs travis uses include several GNU programs that are typically preinstalled in most Linux distributions, including awk
, sed
, sort
, shuf
, and cut
. For older linux distributions, you may need to install a more recent version of GNU core utilities that supports parallelization in sort
.
In addition, there are R dependencies. Install devtools if not installed already:
install.packages("devtools")
Then install conifur (convenience functions for R), converge (conversion tools for genomic data), gyro (wrappers for genomic tools), and travis:
devtools::install_github("dvera/conifur")
devtools::install_github("dvera/converge")
devtools::install_github("dvera/gyro")
devtools::install_github("dvera/travis")
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