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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("sincell")
In most cases, you don't need to download the package archive at all.
sincell
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R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
Bioconductor version: Release (3.1)
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 Juliá <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>, Antonio Rausell<antonio.rausell at isb-sib.ch>
Maintainer: Miguel Juliá <migueljuliamolina at gmail.com>, Antonio Rausell<antonio.rausell at isb-sib.ch>
Citation (from within R,
enter citation("sincell")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("sincell")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sincell")
| R Script | Sincell: Analysis of cell state hierarchies from single-cell RNA-seq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GeneExpression, GeneSetEnrichment, GraphAndNetwork, RNASeq, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (< 6 months) |
| 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 |
| LinkingTo | Rcpp |
| Suggests | BiocStyle, knitr, biomaRt, stringr, monocle |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | sincell_1.0.0.tar.gz |
| Windows Binary | sincell_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | sincell_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | sincell_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/sincell/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/sincell/ |
| Package Downloads Report | Download Stats |
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