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

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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.

Author
Gopuraja Dharmalingam, Tom Carroll
Date of publication
None
Maintainer
Tom Carroll <tc.infomatics@gmail.com>
License
GPL (>= 3)
Version
1.6.0

View on Bioconductor

Man pages

chipExampleBig
Example ChIPprofiles
ChIPprofile
The soggi function and ChIPprofile object.
findconsensusRegions
Plot coverage of points or regions.
groupByOverlaps
Create GRangeslist from all combinations of GRanges
ik_Example
Example Ikaros peaksets
ik_Profiles
Example Ikaros signal over peaksets
manipulateObjects
Join, subset and manipulate ChIPprofile objects
normalise
Normalise ChIPprofiles
normaliseQuantiles
Normalise quantile
Ops
Arithmetic operations
orientBy
Set strand by overlapping or nearest anchor GRanges
plotRegion
Plot regions
pwmCov
Example motif coverage
pwmToCoverage
PWM hits and motif scores as an RLElist
singleGRange
A single GRange

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