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Bioconductor - cicero

cicero

This is the released version of cicero; for the devel version, see cicero.

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

Bioconductor version: Release (3.21)

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 "4.5") and enter:


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

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")

Details biocViews ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software Version 1.26.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 System Requirements URL See More Package Archives

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

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