Package: OGRE 1.9.0

Sven Berres

OGRE: Calculate, visualize and analyse overlap between genomic regions

OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

Authors:Sven Berres [aut, cre], Jörg Gromoll [ctb], Marius Wöste [ctb], Sarah Sandmann [ctb], Sandra Laurentino [ctb]

OGRE_1.9.0.tar.gz
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OGRE.pdf |OGRE.html✨
OGRE/json (API)
NEWS

# Install 'OGRE' in R:

install.packages('OGRE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/svenbioinf/ogre/issues

On BioConductor:OGRE-1.9.0(bioc 3.20)OGRE-1.8.0(bioc 3.19)

bioconductor-package

19 exports 0.49 score 163 dependencies

Last updated 2 months agofrom:b2033ca1d3

Exports:addDataSetFromHub addGRanges covPlot extendGRanges extractPromoters fOverlaps gvizPlot listPredefinedDataSets loadAnnotations makeExampleGRanges makeExampleOGREDataSet OGREDataSet OGREDataSetFromDir plotHist readDataSetFromFolder SHREC subsetGRanges summarizeOverlap sumPlot

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass assertthat backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr DT ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shiny shinyBS shinydashboard shinyFiles snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 xtable XVector yaml zlibbioc

The OGRE user guide

Sven Berres

Rendered fromOGRE.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2022-11-15
Started: 2021-11-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
OGRE package to calculate, analyze and visiualize overlap between annotated genomic region datasets	OGRE-package
Add dataSet from AnnotationHub	addDataSetFromHub
Add GenomicRanges	addGRanges
Coverage plot	covPlot
Extend a GRanges object	extendGRanges
Extract promoter	extractPromoters
Find overlaps	fOverlaps
Generate Gviz plot	gvizPlot
List predefined datasets	listPredefinedDataSets
Load annotation datasets	loadAnnotations
Make an example GRanges dataset	makeExampleGRanges
Make a example OGRE dataset	makeExampleOGREDataSet
BuildOGREDataSet	OGREDataSet
BuildOGREDataSetFromDir	OGREDataSetFromDir
Plot histogram	plotHist
Read dataset(s) from folder	readDataSetFromFolder
SHREC SHiny interface for REgion Comparison	SHREC
Subset a GRanges object	subsetGRanges
Calculates min/max/average overlap	summarizeOverlap
Generate summary plot	sumPlot