cicero

DOI: 10.18129/B9.bioc.cicero    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cicero.

Precict cis-co-accessibility from single-cell chromatin accessibility data

Bioconductor version: 3.9

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

Author: Hannah Pliner [aut, cre], Cole Trapnell [aut]

Maintainer: Hannah Pliner <hpliner at uw.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cicero")

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("cicero")

 

HTML	R Script	Vignette from Cicero Website
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneTarget, ImmunoOncology GeneRegulation, Sequencing, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), monocle, Gviz(>= 1.22.3)
Imports	assertthat (>= 0.2.0), Biobase(>= 2.37.2), BiocGenerics(>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges(>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges(>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors(>= 0.14.7), stats, stringr (>= 1.2.0), tibble (>= 1.4.2), VGAM (>= 1.0-5), utils
LinkingTo
Suggests	AnnotationDbi(>= 1.38.2), knitr, rmarkdown, rtracklayer(>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cicero_1.2.0.tar.gz
Windows Binary	cicero_1.2.0.zip
Mac OS X 10.11 (El Capitan)	cicero_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cicero
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cicero
Package Short Url	https://bioconductor.org/packages/cicero/
Package Downloads Report	Download Stats