singleCellTK
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see singleCellTK.
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
Bioconductor version: 3.13
Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..
Author: David Jenkins [aut] 
, Vidya Akavoor [aut], Salam Alabdullatif [aut], Shruthi Bandyadka [aut], Emma Briars [aut] , Xinyun Cao [aut], Sebastian Carrasco Pro [aut], Tyler Faits [aut], Rui Hong [aut], Mohammed Muzamil Khan [aut], Yusuke Koga [aut, cre], Anastasia Leshchyk [aut], Irzam Sarfraz [aut], Yichen Wang [aut], Zhe Wang [aut], W. Evan Johnson [aut] , Joshua David Campbell [aut]
Maintainer: Yusuke Koga <ykoga07 at bu.edu>
citation("singleCellTK")):
Installation
To install this package, start R (version "4.1") 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 |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, SingleCell, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase |
| Imports | ape, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA(>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer, ROCR, Rtsne, S4Vectors, scater, scMerge(>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, uwot, DropletUtils, scds(>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq(>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap |
| System Requirements | |
| URL | https://compbiomed.github.io/sctk_docs/ |
| Bug Reports | https://github.com/compbiomed/singleCellTK/issues |
See More
| Suggests | testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | celda |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | singleCellTK_2.2.0.tar.gz |
| Windows Binary | singleCellTK_2.2.0.zip |
| macOS 10.13 (High Sierra) | singleCellTK_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/singleCellTK |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org: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 3.13 | Source Archive |