cicero
Predict cis-co-accessibility from single-cell chromatin accessibility data
Bioconductor version: Release (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")):
Installation
To install this package, start R (version "4.4") 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")| Vignette from Cicero Website | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, CellBasedAssays, Clustering, Epigenetics, GeneRegulation, GeneTarget, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cicero_1.22.0.tar.gz |
| Windows Binary (x86_64) | cicero_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | cicero_1.22.0.tgz |
| macOS Binary (arm64) | cicero_1.22.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |