DOI: 10.18129/B9.bioc.cicero    

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

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

Bioconductor version: Development (3.9)

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>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("cicero", version = "3.9")

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


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneTarget, ImmunoOncology GeneRegulation, Sequencing, SingleCell, Software
Version 1.1.5
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
Suggests AnnotationDbi(>= 1.38.2), knitr, rmarkdown, rtracklayer(>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
Depends On Me
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