singleCellTK
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.
Interactive Analysis of Single Cell RNA-Seq Data
Bioconductor version: 3.9
Run common single cell analysis directly through your browser including differential expression, downsampling analysis, and clustering.
Author: David Jenkins
Maintainer: David Jenkins <dfj at bu.edu>
Citation (from within R, enter
citation("singleCellTK")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("singleCellTK")
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("singleCellTK")| 1. Introduction to singleCellTK | HTML | R Script |
| 2. Processing and Visualizing Data in the Single Cell Toolkit | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software |
| Version | 1.4.2 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase |
| Imports | ape, colourpicker, cluster, ComplexHeatmap, data.table, DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly, RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, shinycssloaders, shinythemes, umap |
| System Requirements | |
| URL | https://compbiomed.github.io/sctk_docs/ |
| Bug Reports | https://github.com/compbiomed/singleCellTK/issues |
See More
| Suggests | testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase, lintr |
| 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 | singleCellTK_1.4.2.tar.gz |
| Windows Binary | singleCellTK_1.4.2.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | singleCellTK_1.4.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/singleCellTK |
| Source Repository (Developer Access) | git clone [email protected]:packages/singleCellTK |
| Bioc Package Browser | https://code.bioconductor.org/browse/singleCellTK/ |
| Package Short Url | https://bioconductor.org/packages/singleCellTK/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |