recipe bioconductor-singlecelltk

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/singleCellTK.html

License

MIT + file LICENSE

Recipe

/bioconductor-singlecelltk/meta.yaml

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..

package bioconductor-singlecelltk

Versions

2.2.0-0,  2.0.0-1,  2.0.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-1,  1.2.3-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-batchelor >=1.8.0,<1.9.0

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-celda >=1.8.0,<1.9.0

• bioconductor-celldex >=1.2.0,<1.3.0

• bioconductor-complexheatmap >=2.8.0,<2.9.0

• bioconductor-delayedarray >=0.18.0,<0.19.0

• bioconductor-delayedmatrixstats >=1.14.0,<1.15.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-dropletutils >=1.12.0,<1.13.0

• bioconductor-experimenthub >=2.0.0,<2.1.0

• bioconductor-fishpond >=1.8.0,<1.9.0

• bioconductor-ggtree >=3.0.0,<3.1.0

• bioconductor-gseabase >=1.54.0,<1.55.0

• bioconductor-gsva >=1.40.0,<1.41.0

• bioconductor-gsvadata >=1.28.0,<1.29.0

• bioconductor-limma >=3.48.0,<3.49.0

• bioconductor-mast >=1.18.0,<1.19.0

• bioconductor-multtest >=2.48.0,<2.49.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-scater >=1.20.0,<1.21.0

• bioconductor-scdblfinder >=1.6.0,<1.7.0

• bioconductor-scds >=1.8.0,<1.9.0

• bioconductor-scmerge >=1.8.0,<1.9.0

• bioconductor-scran >=1.20.0,<1.21.0

• bioconductor-scrnaseq >=2.6.0,<2.7.0

• bioconductor-singlecellexperiment >=1.14.0,<1.15.0

• bioconductor-singler >=1.6.0,<1.7.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• bioconductor-sva >=3.40.0,<3.41.0

• bioconductor-tenxpbmcdata >=1.10.0,<1.11.0

• bioconductor-tximport >=1.20.0,<1.21.0

• bioconductor-zinbwave >=1.14.0,<1.15.0

• r-ape

• r-base >=4.1,<4.2.0a0

• r-circlize

• r-cluster

• r-colorspace

• r-colourpicker

• r-cowplot

• r-data.table

• r-dplyr

• r-dt

• r-enrichr

• r-fields

• r-ggplot2

• r-ggplotify

• r-ggrepel

• r-gridextra

• r-igraph

• r-kernsmooth

• r-magrittr

• r-matrix

• r-matrixstats

• r-metap

• r-msigdbr

• r-plotly

• r-r.utils

• r-rcolorbrewer

• r-reshape2

• r-reticulate >=1.14

• r-rmarkdown

• r-rocr

• r-rtsne

• r-seurat >=3.1.3

• r-shiny

• r-shinyalert

• r-shinycssloaders

• r-shinyjs

• r-uwot

• r-withr

• r-yaml

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-singlecelltk

and update with:

conda update bioconductor-singlecelltk

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-singlecelltk:<tag>

(see bioconductor-singlecelltk/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-singlecelltk/README.html)