epiSeeker
This is the development version of epiSeeker; to use it, please install the devel version of Bioconductor.
epiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data
Bioconductor version: Development (3.23)
This package implements functions to analyze multi-omics epigenetic data. Data of fragment type and base type are supported by epiSeeker. It provides functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods to estimate the significance of overlap among peak data sets, and motif analysis. It incorporates the GEO database for users to compare their own dataset with those deposited in the database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, overlap of peaks or genes, and the single-base resolution epigenetic data by considering the strand, motif, and additional information.
Author: Guangchuang Yu [aut, cre, fnd]
, Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb], Chun-Hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("epiSeeker")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("epiSeeker")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("epiSeeker")| epiSeeker.html | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, ChIPSeq, Coverage, GeneRegulation, MotifAnnotation, MultipleComparison, Software, Visualization |
| Version | 0.99.14 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | AnnotationDbi, aplot, bsseq, BiocGenerics, Biostrings, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, graphics, grDevices, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, RSQLite, rtracklayer, S4Vectors, scales, stats, SummarizedExperiment, tibble, tidyselect, tidyr, utils, yulab.utils (>= 0.2.0), grid |
| System Requirements | |
| URL | https://github.com/YuLab-SMU/epiSeeker |
| Bug Reports | https://github.com/YuLab-SMU/epiSeeker/issues |
See More
| Suggests | ape, BSgenome, BSgenome.Hsapiens.UCSC.hg38, clusterProfiler, data.table, GEOmetadb, GEOquery, gggenes, ggimage, ggiraph, ggplotify, ggtree, gginnards, gridBase, gtools, ggupset, ggVennDiagram, JASPAR2024, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat, TFBSTools, TxDb.Hsapiens.UCSC.hg38.knownGene, universalmotif |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | epiSeeker_0.99.14.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | epiSeeker_0.99.14.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/epiSeeker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epiSeeker |
| Bioc Package Browser | https://code.bioconductor.org/browse/epiSeeker/ |
| Package Short Url | https://bioconductor.org/packages/epiSeeker/ |
| Package Downloads Report | Download Stats |