cicero

This is the development version of cicero; for the stable release version, see cicero.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Details

biocViews	ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software
Version	1.19.0
In Bioconductor since	BioC 3.8 (R-3.5) (5 years)
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, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils
Linking To
Suggests	AnnotationDbi(>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer(>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
System Requirements
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_1.19.0.tar.gz
Windows Binary	cicero_1.19.0.zip (64-bit only)
macOS Binary (x86_64)	cicero_1.19.0.tgz
macOS Binary (arm64)	cicero_1.19.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cicero
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cicero
Bioc Package Browser	https://code.bioconductor.org/browse/cicero/
Package Short Url	https://bioconductor.org/packages/cicero/
Package Downloads Report	Download Stats