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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 (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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Vignette from Cicero Website HTML R Script
Reference Manual PDF


biocViews ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (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
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Suggests AnnotationDbi(>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer(>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
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Follow Installation instructions to use this package in your R session.

Source Package cicero_1.21.0.tar.gz
Windows Binary cicero_1.21.0.zip (64-bit only)
macOS Binary (x86_64) cicero_1.21.0.tgz
macOS Binary (arm64)
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/
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