recipe bioconductor-iloreg

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Homepage

https://bioconductor.org/packages/3.14/bioc/html/ILoReg.html

License

GPL-3

Recipe

/bioconductor-iloreg/meta.yaml

ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.

package bioconductor-iloreg

Versions

1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

Depends

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-aricode

• r-base >=4.1,<4.2.0a0

• r-cluster

• r-cowplot

• r-dendextend

• r-desctools

• r-dorng

• r-dosnow

• r-dplyr

• r-fastcluster

• r-foreach

• r-ggplot2

• r-liblinear

• r-matrix

• r-paralleldist

• r-pheatmap

• r-plyr

• r-reshape2

• r-rspectra

• r-rtsne

• r-scales

• r-sparsem

• r-umap

Required By

Installation

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

conda install bioconductor-iloreg

and update with:

conda update bioconductor-iloreg

or use the docker container:

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

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

Download stats

Link to this page

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