cicero

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

Bioconductor version: 3.23 · Package version: 1.30.0

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.

Installation

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

BiocManager::install("cicero")

Details

Maintainer	Hannah Pliner <hpliner@uw.edu>
Author	Hannah Pliner [aut, cre], Cole Trapnell [aut]
License	MIT + file LICENSE
Downloads rank	602
Source branch	RELEASE_3_23
biocViews	ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software

Documentation

Single Cell ATAC-seq Analysis with Cicero

Download

Source package

Dependencies

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

Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr