recipe bioconductor-singlecelltk

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/singleCellTK.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-singlecelltk/meta.yaml

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

package bioconductor-singlecelltk

Versions:

2.8.0-0,  2.4.0-0,  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-annotationhub >=3.6.0,<3.7.0

• bioconductor-batchelor >=1.14.0,<1.15.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-celda >=1.14.0,<1.15.0

• bioconductor-celldex >=1.8.0,<1.9.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-delayedarray >=0.24.0,<0.25.0

• bioconductor-delayedmatrixstats >=1.20.0,<1.21.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-dropletutils >=1.18.0,<1.19.0

• bioconductor-ensembldb >=2.22.0,<2.23.0

• bioconductor-experimenthub >=2.6.0,<2.7.0

• bioconductor-fishpond >=2.4.0,<2.5.0

• bioconductor-ggtree >=3.6.0,<3.7.0

• bioconductor-gseabase >=1.60.0,<1.61.0

• bioconductor-gsva >=1.46.0,<1.47.0

• bioconductor-gsvadata >=1.34.0,<1.35.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-mast >=1.24.0,<1.25.0

• bioconductor-multtest >=2.54.0,<2.55.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-scater >=1.26.0,<1.27.0

• bioconductor-scdblfinder >=1.12.0,<1.13.0

• bioconductor-scds >=1.14.0,<1.15.0

• bioconductor-scmerge >=1.14.0,<1.15.0

• bioconductor-scran >=1.26.0,<1.27.0

• bioconductor-scrnaseq >=2.12.0,<2.13.0

• bioconductor-scuttle >=1.8.0,<1.9.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-singler >=2.0.0,<2.1.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-sva >=3.46.0,<3.47.0

• bioconductor-tenxpbmcdata >=1.16.0,<1.17.0

• bioconductor-trajectoryutils >=1.6.0,<1.7.0

• bioconductor-tscan >=1.36.0,<1.37.0

• bioconductor-tximport >=1.26.0,<1.27.0

• bioconductor-zinbwave >=1.20.0,<1.21.0

• r-ape

• r-base >=4.2,<4.3.0a0

• 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-plyr

• r-r.utils

• r-reshape2

• r-reticulate >=1.14

• r-rlang

• r-rmarkdown

• r-rocr

• r-rtsne

• r-seurat >=3.1.3

• r-shiny

• r-shinyalert

• r-shinycssloaders

• r-shinyjs

• r-soupx

• r-tibble

• r-vam >=0.5.3

• r-withr

• r-yaml

Required By:

Installation

With an activated Bioconda channel (see 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)