https://github.com/bioconductor-source/sincell
Science Score: 13.0%
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Low similarity (11.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 572 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Sincell
R/Bioconductor package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
Bioconductor version: Release (3.8)
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
Maintainer: Miguel Julia
Citation (from within R, enter citation("sincell")):
Juliá M, Telenti A, Rausell A (2014). “Sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data.” bioRxiv. http://dx.doi.org/.
Installation
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sincell", version = "3.8")
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")
| Document | Script | Title | | :-------------: |:-------------:| :------------------| | PDF | R Script | Sincell: Analysis of cell state hierarchies from single-cell RNA-seq | | PDF | - | Reference Manual | | Text | - | NEWS |
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Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
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Dependencies
- R >= 3.0.2 depends
- igraph * depends
- MASS * imports
- Rcpp >= 0.11.2 imports
- Rtsne * imports
- TSP * imports
- cluster * imports
- entropy * imports
- fastICA * imports
- fields * imports
- ggplot2 * imports
- parallel * imports
- proxy * imports
- reshape2 * imports
- scatterplot3d * imports
- statmod * imports
- BiocStyle * suggests
- biomaRt * suggests
- knitr * suggests
- monocle * suggests
- stringr * suggests