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

Files in this package

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.

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