Package: DegCre 1.1.0

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_1.1.0.tar.gz
DegCre_1.1.0.zip(r-4.5)DegCre_1.1.0.zip(r-4.4)DegCre_1.1.0.zip(r-4.3)
DegCre_1.1.0.tgz(r-4.4-any)DegCre_1.1.0.tgz(r-4.3-any)
DegCre_1.1.0.tar.gz(r-4.5-noble)DegCre_1.1.0.tar.gz(r-4.4-noble)
DegCre_1.1.0.tgz(r-4.4-emscripten)DegCre_1.1.0.tgz(r-4.3-emscripten)
DegCre.pdf |DegCre.html✨
DegCre/json (API)
NEWS

# 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-1.1.0(bioc 3.20)DegCre-1.0.0(bioc 3.19)

bioconductor-package

14 exports 1.24 score 95 dependencies

Last updated 2 months agofrom:ee9a9ae2ce

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

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops cachem cli codetools colorspace cpp11 crayon curl data.table DelayedArray digest dplyr fansi farver fastmap formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggplotify glue gridGraphics gtable httr InteractionSet IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plotgardener plyranges purrr R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray strawr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml yulab.utils zlibbioc

DegCre Introduction and Examples

Brian S. Roberts

Rendered fromdegcre_introduction_and_examples.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-03-18
Started: 2023-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Raw Association Probability Odds Ratio (OR)	calcRawAssocProbOR
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