soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.

AuthorGopuraja Dharmalingam, Tom Carroll
Date of publicationNone
MaintainerTom Carroll <tc.infomatics@gmail.com>
LicenseGPL (>= 3)
Version1.6.0

View on Bioconductor

Functions

cbind,ChIPprofile-method Man page
c,ChIPprofile-method Man page
chipExampleBig Man page
ChIPprofile Man page
[[,ChIPprofile,ANY,missing-method Man page
ChIPprofile-ChIPprofile Man page
ChIPprofile-class Man page
$,ChIPprofile-method Man page
findconsensusRegions Man page
groupByOverlaps Man page
ik_Example Man page
ik_Profiles Man page
log2,ChIPprofile-method Man page
log,ChIPprofile-method Man page
makeMotifScoreRle Man page
mean,ChIPprofile-method Man page
normalise Man page
normalise.ChIPprofile Man page
normalise,ChIPprofile,character,numeric-method Man page
normalise,ChIPprofile-method Man page
normaliseQuantiles Man page
normaliseQuantiles.ChIPprofile Man page
normaliseQuantiles,ChIPprofile-method Man page
Ops,ChIPprofile,ChIPprofile-method Man page
Ops,ChIPprofile,numeric-method Man page
Ops,numeric,ChIPprofile-method Man page
orientBy Man page
plotRegion Man page
plotRegion.ChIPprofile Man page
plotRegion,ChIPprofile-method Man page
pwmCov Man page
pwmToCoverage Man page
rbind,ChIPprofile-method Man page
regionPlot Man page
singleGRange Man page
soggi Man page
summitPipeline Man page

Files

soGGi/DESCRIPTION
soGGi/NAMESPACE
soGGi/R
soGGi/R/allClasses.r
soGGi/R/motifTools.R
soGGi/R/peakTransforms.r
soGGi/R/plots.R soGGi/R/soggi.R
soGGi/build
soGGi/build/vignette.rds
soGGi/data
soGGi/data/chipExampleBig.rda
soGGi/data/datalist
soGGi/data/ik_Example.rda
soGGi/data/ik_Profiles.rda
soGGi/data/pwmCov.rda
soGGi/data/singleGRange.rda
soGGi/inst
soGGi/inst/NEWS.Rd
soGGi/inst/doc
soGGi/inst/doc/soggi.R
soGGi/inst/doc/soggi.Rnw
soGGi/inst/doc/soggi.pdf
soGGi/man
soGGi/man/ChIPprofile.Rd soGGi/man/Ops.Rd soGGi/man/chipExampleBig.Rd soGGi/man/findconsensusRegions.Rd soGGi/man/groupByOverlaps.Rd soGGi/man/ik_Example.Rd soGGi/man/ik_Profiles.Rd soGGi/man/manipulateObjects.Rd soGGi/man/normalise.Rd soGGi/man/normaliseQuantiles.Rd soGGi/man/orientBy.Rd soGGi/man/plotRegion.Rd soGGi/man/pwmCov.Rd soGGi/man/pwmToCoverage.Rd soGGi/man/singleGRange.Rd
soGGi/tests
soGGi/tests/testthat
soGGi/tests/testthat.R
soGGi/tests/testthat/test_manipulations.R
soGGi/tests/testthat/test_operations.r
soGGi/tests/testthat/test_plotting.R
soGGi/vignettes
soGGi/vignettes/soggi.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.