Damsel
This is the development version of Damsel; for the stable release version, see Damsel.
Damsel: an end to end analysis of DamID
Bioconductor version: Development (3.21)
Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.
Author: Caitlin Page [aut, cre] (ORCID:
Maintainer: Caitlin Page <caitlin.page at petermac.org>
citation("Damsel")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("Damsel")
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("Damsel")| Damsel-workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialMethylation, GenePrediction, GeneSetEnrichment, PeakDetection, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils |
| System Requirements | |
| URL | https://github.com/Oshlack/Damsel |
| Bug Reports | https://github.com/Oshlack/Damsel |
See More
| Suggests | BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene |
| 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 | Damsel_1.3.0.tar.gz |
| Windows Binary (x86_64) | Damsel_1.3.0.zip (64-bit only) |
| macOS Binary (x86_64) | Damsel_1.3.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Damsel |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Damsel |
| Bioc Package Browser | https://code.bioconductor.org/browse/Damsel/ |
| Package Short Url | https://bioconductor.org/packages/Damsel/ |
| Package Downloads Report | Download Stats |