recipe bioconductor-irisfgm

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-irisfgm/meta.yaml

Single-cell RNA-Seq data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of functional gene modules (FGM) can help to understand gene interactive networks and complex biological processes. QUBIC2 is recognized as one of the most efficient and effective tools for FGM identification from scRNA-Seq data. However, its availability is limited to a C implementation, and its applicative power is affected by only a few downstream analyses functionalities. We developed an R package named IRIS-FGM (integrative scRNA-Seq interpretation system for functional gene module analysis) to support the investigation of FGMs and cell clustering using scRNA-Seq data. Empowered by QUBIC2, IRIS-FGM can identify co-expressed and co-regulated FGMs, predict types/clusters, identify differentially expressed genes, and perform functional enrichment analysis. It is noteworthy that IRIS-FGM also applies Seurat objects that can be easily used in the Seurat vignettes.

package bioconductor-irisfgm

Versions:

1.6.0-0,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-desingle >=1.18.0,<1.19.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-org.mm.eg.db >=3.16.0,<3.17.0

• bioconductor-scater >=1.26.0,<1.27.0

• bioconductor-scran >=1.26.0,<1.27.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-adaptgauss

• r-anocva

• r-base >=4.2,<4.3.0a0

• r-colorspace

• r-drimpute

• r-ggplot2

• r-ggpubr

• r-ggraph

• r-igraph

• r-knitr

• r-matrix

• r-mcl

• r-mixtools

• r-pheatmap

• r-polychrome

• r-rcolorbrewer

• r-rcpp >=1.0.0

• r-seurat

Required By:

Installation

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

conda install bioconductor-irisfgm

and update with:

conda update bioconductor-irisfgm

or use the docker container:

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

(see bioconductor-irisfgm/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-irisfgm/README.html)