UMI4Cats
This is the released version of UMI4Cats; for the devel version, see UMI4Cats.
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Bioconductor version: Release (3.23)
UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.
Author: Mireia Ramos-Rodriguez [aut, cre]
, Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]
Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at gmail.com>
citation("UMI4Cats")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("UMI4Cats")
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("UMI4Cats")| Analyzing UMI-4C data with UMI4Cats | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), SummarizedExperiment |
| Imports | magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics |
| System Requirements | |
| URL | https://github.com/Pasquali-lab/UMI4Cats |
| Bug Reports | https://github.com/Pasquali-lab/UMI4Cats/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat |
| 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 | UMI4Cats_1.22.0.tar.gz |
| Windows Binary (x86_64) | UMI4Cats_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | UMI4Cats_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | UMI4Cats_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/UMI4Cats |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/UMI4Cats |
| Bioc Package Browser | https://code.bioconductor.org/browse/UMI4Cats/ |
| Package Short Url | https://bioconductor.org/packages/UMI4Cats/ |
| Package Downloads Report | Download Stats |