recipe bioconductor-iloreg

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

Homepage:

https://bioconductor.org/packages/3.17/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:

1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-aricode:

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-cowplot:

depends r-dendextend:

depends r-desctools:

depends r-dorng:

depends r-dosnow:

depends r-dplyr:

depends r-fastcluster:

depends r-foreach:

depends r-ggplot2:

depends r-liblinear:

depends r-matrix:

depends r-paralleldist:

depends r-pheatmap:

depends r-plyr:

depends r-reshape2:

depends r-rspectra:

depends r-rtsne:

depends r-scales:

depends r-sparsem:

depends r-umap:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-iloreg

and update with::

   mamba update bioconductor-iloreg

To create a new environment, run:

mamba create --name myenvname bioconductor-iloreg

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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Link to this page

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