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 (version "3.5") and enter:

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

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 1.0.15
In Bioconductor since BioC 3.8 (R-3.5) (< 6 months)
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_1.0.15.tar.gz
Windows Binary cicero_1.0.15.zip
Mac OS X 10.11 (El Capitan) cicero_1.0.15.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: