cicero

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

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

Bioconductor version: Development (3.24)

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")):

Hannah Pliner, Cole Trapnell. cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data. doi:10.18129/B9.bioc.cicero, R package version 1.31.0, https://bioconductor.org/packages/cicero.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software
Version	1.31.0
In Bioconductor since	BioC 3.8 (R-3.5) (8 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
System Requirements
URL

Suggests	AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	cicero_1.31.0.tar.gz
Windows Binary (x86_64)	cicero_1.31.0.zip
macOS Binary (big-sur-x86_64)	cicero_1.31.0.tgz
macOS Binary (sonoma-arm64)	cicero_1.31.0.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