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 <firstname.lastname@example.org>|
|License||GPL (>= 3)|
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