recipe bioconductor-monocle

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-monocle/meta.yaml

Links:

biotools: monocle

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

package bioconductor-monocle

Versions:

2.26.0-1,  2.26.0-0,  2.22.0-2,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-2,  2.18.0-1,  2.16.0-0, 

2.26.0-1,  2.26.0-0,  2.22.0-2,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-2,  2.18.0-1,  2.16.0-0,  2.14.0-1,  2.12.0-1,  2.10.0-0,  2.8.0-0,  2.6.0-0,  2.4.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocviews >=1.66.0,<1.67.0

• bioconductor-hsmmsinglecell >=1.18.0,<1.19.0

• bioconductor-limma >=3.54.0,<3.55.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-cluster

• r-combinat

• r-ddrtree >=0.1.4

• r-dplyr

• r-fastica

• r-ggplot2 >=1.0.0

• r-igraph >=1.0.1

• r-irlba >=2.0.0

• r-leidenbase >=0.1.9

• r-mass

• r-matrix >=1.2-6

• r-matrixstats

• r-pheatmap

• r-plyr

• r-proxy

• r-qlcmatrix

• r-rann >=2.5

• r-rcpp >=0.12.0

• r-reshape2

• r-rtsne

• r-slam

• r-stringr

• r-tibble

• r-vgam >=1.0-6

• r-viridis

Required By:

• bioconductor-cicero

• bioconductor-usort

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-monocle

and update with:

conda update bioconductor-monocle

or use the docker container:

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

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

Download stats

Link to this page

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