Package: DegCre 1.9.0

Brian S. Roberts

DegCre: Probabilistic association of DEGs to CREs from differential data

DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

Authors:Brian S. Roberts [aut, cre]

DegCre_1.9.0.tar.gz
DegCre_1.9.0.zip(r-4.7)DegCre_1.9.0.zip(r-4.6)DegCre_1.9.0.zip(r-4.5)
DegCre_1.9.0.tgz(r-4.6-any)DegCre_1.9.0.tgz(r-4.5-any)
DegCre_1.9.0.tar.gz(r-4.7-any)DegCre_1.9.0.tar.gz(r-4.6-any)
DegCre_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DegCre/json (API)

# Install 'DegCre' in R:

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

Bug tracker:https://github.com/briansroberts/degcre/issues

Datasets:

DexNR3C1 - DegCre input data for examples.

On BioConductor:DegCre-1.9.0(bioc 3.24)DegCre-1.8.0(bioc 3.23)

geneexpression generegulation atacseq chipseq dnaseseq rnaseq

4.88 score 5 stars 5 scripts 267 downloads 17 exports 111 dependencies

Last updated from:60bbe80337. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	375
linux-devel-x86_64	NOTE	662
source / vignettes	OK	479
linux-release-x86_64	NOTE	601
macos-release-arm64	NOTE	493
macos-oldrel-arm64	NOTE	465
windows-devel	NOTE	734
windows-release	NOTE	799
windows-oldrel	NOTE	731
wasm-release	OK	311

Exports:calcAssocProbOR calcRawAssocProbOR changeColorAlpha collapseDegCreToGene convDegCreResListToCreGeneScoreGR convertDegCreDataFrame convertdegCreResListToGInteraction degCrePRAUC getAssocDistHits getDistBinNullAssocProb getExpectAssocPerDEG optimizeAlphaDegCre plotBrowserDegCre plotDegCreAssocProbVsDist plotDegCreBinHeuristic plotExpectedAssocsPerDeg runDegCre

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray digest dir.expiry dplyr farver fastmap filelock formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggplotify glue gridGraphics gtable httr InteractionSet IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db pillar pkgconfig plotgardener plyr plyranges png purrr qvalue R6 rappdirs RColorBrewer Rcpp RCurl reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyselect TxDb.Hsapiens.UCSC.hg38.knownGene UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml yulab.utils

DegCre Introduction and Examples

Rendered fromdegcre_introduction_and_examples.Rmdusingknitr::rmarkdown

Last update: 2024-08-22
Started: 2023-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Odds-ratio	calcAssocProbOR
Calculate Raw Association Probability Odds Ratio (OR)	calcRawAssocProbOR
Collapse DegCre associations to a single TSS per gene	collapseDegCreToGene
Convert a degCreResList to a creGeneScoreGR	convDegCreResListToCreGeneScoreGR
Convert DegCre Results List to DataFrame	convertDegCreDataFrame
Convert DegCre Results List to GInteractions Object	convertdegCreResListToGInteraction
DegCre	DegCre-package DegCre
Calculate PR AUC for DegCre results.	degCrePRAUC
DegCre input data for examples.	DexNR3C1
Get Associations and Distances Between Genomic Regions	getAssocDistHits
Calculate Null Association Probability for Each Distance Bin	getDistBinNullAssocProb
Get Expected Associations per DEG	getExpectAssocPerDEG
Run DegCre with DEG alpha optimization.	optimizeAlphaDegCre
Make Browser Plots from DegCre Results	plotBrowserDegCre
Plot DegCre Association Probability vs. Binned Genomic Distance	plotDegCreAssocProbVsDist
Plot DegCre Bin Algorithm Statistics	plotDegCreBinHeuristic
Plot Histogram of Expected Associations per DEG	plotExpectedAssocsPerDeg
Generate DegCre associations	runDegCre