cicero

DOI: 10.18129/B9.bioc.cicero    

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

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("cicero")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cicero", version = "3.8")

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, GeneRegulation, GeneTarget, Sequencing, SingleCell, Software
Version 1.0.11
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_1.0.11.tar.gz
Windows Binary cicero_1.0.11.zip
Mac OS X 10.11 (El Capitan) cicero_1.0.11.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 http://bioconductor.org/packages/cicero/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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