damidBind
This is the development version of damidBind; to use it, please install the devel version of Bioconductor.
Differential Binding and Expression Analysis for DamID-seq Data
Bioconductor version: Development (3.23)
The damidBind package provides a straightforward formal analysis pipeline to analyse and explore differential DamID binding, gene transcription or chromatin accessibility between two conditions. The package imports processed data from DamID-seq experiments, either as external raw files in the form of binding bedGraphs and GFF/BED peak calls, or as internal lists of GRanges objects. After optionally normalising data, combining peaks across replicates and determining per-replicate peak occupancy, the package links bound loci to nearby genes. For RNA Polymerase DamID data, the package calculates occupancy over genes, and optionally calcualates the FDR of significantly-enriched gene occupancy. damidBind then uses either limma (for conventional log2 ratio DamID binding data) or NOIseq (for counts-based CATaDa chromatin accessibility data) to identify differentially-enriched regions, or differentially epxressed genes, between two conditions. The package provides a number of visualisation tools (volcano plots, Gene Ontology enrichment plots via ClusterProfiler and proportional Venn diagrams via BioVenn for downstream data exploration and analysis. An powerful, interactive IGV genome browser interface (powered by Shiny and igvShiny) allows users to rapidly and intuitively assess significant differentially-bound regions in their genomic context.
Author: Owen Marshall [aut, cre]
Maintainer: Owen Marshall <owen.marshall at utas.edu.au>
citation("damidBind")):
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("damidBind")
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("damidBind")| damidBind | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Epigenetics, GeneExpression, GeneRegulation, Sequencing, Software, Transcription, Visualization |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | ggplot2, ggrepel, dplyr, tibble, stringr, tools, rlang, BiocParallel, AnnotationHub, DBI, ensembldb, GenomeInfoDb, IRanges, GenomicRanges, S4Vectors, rtracklayer, limma, NOISeq, BioVenn, clusterProfiler, enrichplot, forcats, scales, colorspace, ggnewscale, methods, stats, igvShiny, shiny, DT, RcppHNSW |
| System Requirements | |
| URL | https://marshall-lab.org/damidBind |
| Bug Reports | https://github.com/marshall-lab/damidBind/issues |
See More
| Suggests | testthat, knitr, htmltools, rmarkdown, BiocStyle, org.Dm.eg.db |
| 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 | damidBind_0.99.9.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | damidBind_0.99.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/damidBind |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/damidBind |
| Bioc Package Browser | https://code.bioconductor.org/browse/damidBind/ |
| Package Short Url | https://bioconductor.org/packages/damidBind/ |
| Package Downloads Report | Download Stats |