GenomicInteractions v1.6.2
R package for handling genomic interaction data
R package for handling Genomic interaction data, such as
ChIA-PET/Hi-C, annotating genomic features with interaction
information and producing various plots / statistics.
Readme
##GenomicInteractions
GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data. It provides simple annotation of genomic features which interfaces with existing Bioconductor packages, as well as numerous plotting functions and summary statistics.
###Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")
To install the latest version from this repository using the devtools package:
library(devtools)
install_github("ComputationalRegulatoryGenomicsICL/GenomicInteractions")
###Bioconductor links and documentation
The bioconductor page contains documentation for the released package: Bioconductior Release 3.0
To view example Hi-C and ChIA-PET analysis for using this package on your system, start R and enter:
browseVignettes("GenomicInteractions")
###Citation
From within R, enter citation("GenomicInteractions"):
Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., and Lenhard, B. (2014). GenomicInteractions: R package for handling genomic interaction data. R package version 1.0.0.
###Contributing
We welcome contributions in any form: suggestions, issues, bugfixes. Pull requests should be made to the development branch.
Functions in GenomicInteractions
| Name | Description | |
| export.bed12 | Export interactions in BED12 format. | |
| export.igraph | Export interactions to an igraph object. | |
| GenomicInteractions-package | A package for looking at genomic interaction data. | |
| thymus_enh | Putative enhancers from mouse thymus data | |
| get_binom_ligation_threshold | get self ligation threshold with binomial test | |
| get_self_ligation_threshold | Get self ligation threshold with SD method from Heidari et al | |
| sum,GInteractions-method | Return the total number of interactions in a GInteractions GIObject | |
| availableDisplayPars | The default display parameters for a track object class can be queries using the availableDisplayPars function. | |
| asBED,GInteractions-method | Coerce to BED structure | |
| hg19.refseq.transcripts | Human Refseq transcripts from chr 17-18 | |
| calculateDistances | Calculate interaction distances | |
| subsetByFeatures | Subset a GInteractions object by features | |
| export.bedpe | Export interactions in BED Paired-End format. | |
| InteractionTrack-class | A class to hold chromatin interaction data for a specific genomic region. | |
| plotInteractionAnnotations | Plot a donut plot of interaction types for an annotated GInteractions object | |
| annotateInteractions | Annotate the interactions in a GInteractions object | |
| countsBetweenAnchors | Summarise interactions between defined anchors | |
| sameStrand | Tests whether anchors have the same strand. | |
| summariseByFeaturePairs | Summarise the number of interactions between two sets of features. | |
| mm9_refseq_promoters | Mouse Refseq promoters from chr 14-15 | |
| plotDists | Plots a histogram of interaction distances for a GInteractions Object | |
| viewPoint | Virtual 4C viewpoint | |
| updateObject,GenomicInteractions-method | updateObject method for GenomicInteractions 1.3.7 and earlier | |
| annotateAnchors | Annotate anchors - DEPRECATED | |
| plotViewpoint | Plot coverage around a virtual 4C viewpoint | |
| removeDups | Remove all but one occurences of a duplicated interaction | |
| is.pp | Interaction Type Helpers | |
| annotateRegions | Annotate regions | |
| categoriseInteractions | Get the numbers of interaction types existing in your data | |
| export.chiasig | Export interactions in a BEDPE-like format for use with ChiaSig | |
| getters | Functions to access data held in a GenomicInteractions object. | |
| resetAnnotations | Reset annotations made to a GInteractions object | |
| GenomicInteractions-class | A S4 class to represent interactions between genomic regions. | |
| plotCisTrans | Plots the percentages of cis and trans interactions for a GInteractions object as a donut plot. | |
| makeGenomicInteractionsFromFile | Function to create GenomicInteraction objects from a file | |
| summariseByFeatures | Summary statistics of interactions for a given feature set | |
| setters | Functions to set data held in a GInteractions object. | |
| plotAvgViewpoint | Plot coverage around a set of virtual 4C viewpoints | |
| GenomicInteractions | Function to create a GenomicInteractions object | |
| InteractionTrack | Constructor to create an InteractionTrack object | |
| hic_example_data | Example HiC dataset | |
| plotCounts | Plot a bar chart of the number of interactions supported by different numbers of reads in your data. | |
| plotSummaryStats | Plot summary statistics for a GInteractions object | |
| No Results! | ||
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Details
| Type | Package |
| URL | https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/ |
| Date | 2015-07-20 |
| VignetteBuilder | knitr |
| biocViews | Software,Infrastructure,DataImport,DataRepresentation,HiC |
| License | GPL-3 |
| RoxygenNote | 5.0.1 |
| depends | base (>= 3.3) , InteractionSet , R (>= 3.3) |
| imports | Biobase , BiocGenerics (>= 0.15.3) , data , data.table , dplyr , GenomeInfoDb , GenomicRanges , ggplot2 , graphics , grid , gridExtra , Gviz , igraph , IRanges , methods , Rsamtools , rtracklayer , S4Vectors , stats , stringr , utils |
| suggests | BiocStyle , knitr , testthat |
| Contributors | E, M, Harmston, Perry, Baresic, Lenhard, B, N, Ing-Simmons, A |
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