sincell
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
Bioconductor version: Release (3.20)
Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.
Author: Miguel Julia <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>, Antonio Rausell <antonio.rausell at institutimagine.org>
Maintainer: Miguel Julia <migueljuliamolina at gmail.com>, Antonio Rausell<antonio.rausell at institutimagine.org>
citation("sincell")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sincell")
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("sincell")| Sincell: Analysis of cell state hierarchies from single-cell RNA-seq | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.2), igraph |
| Imports | Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod |
| System Requirements | |
| URL | http://bioconductor.org/ |
See More
| Suggests | BiocStyle, knitr, biomaRt, stringr, monocle |
| Linking To | Rcpp |
| 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 | sincell_1.38.0.tar.gz |
| Windows Binary (x86_64) | sincell_1.38.0.zip (64-bit only) |
| macOS Binary (x86_64) | sincell_1.38.0.tgz |
| macOS Binary (arm64) | sincell_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sincell |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sincell |
| Bioc Package Browser | https://code.bioconductor.org/browse/sincell/ |
| Package Short Url | https://bioconductor.org/packages/sincell/ |
| Package Downloads Report | Download Stats |