UMI4Cats
This is thereleased version of UMI4Cats; for the devel version, seeUMI4Cats.
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0001-8083-2445, Marc Subirana-Granes [aut], Lorenzo Pasquali [aut]
Maintainer: Mireia Ramos-Rodriguez <mireiarr9 at gmail.com>
citation("UMI4Cats")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("UMI4Cats")For older versions of R, please refer to the appropriateBioconductor 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 | 1.20.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | UMI4Cats_1.20.0.tar.gz |
| Windows Binary (x86_64) | UMI4Cats_1.20.0.zip |
| macOS Binary (x86_64) | UMI4Cats_1.20.0.tgz |
| macOS Binary (arm64) | UMI4Cats_1.20.0.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 |