Package Recipe 'bioconductor-irisfgm'

recipe bioconductor-irisfgm

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

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

1.8.0-0, 1.6.0-0, 1.2.0-2, 1.2.0-1, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-annotationdbi >=1.62.0,<1.63.0
on bioconductor-clusterprofiler >=4.8.0,<4.9.0
on bioconductor-desingle >=1.20.0,<1.21.0
on bioconductor-org.hs.eg.db >=3.17.0,<3.18.0
on bioconductor-org.mm.eg.db >=3.17.0,<3.18.0
on bioconductor-scater >=1.28.0,<1.29.0
on bioconductor-scran >=1.28.0,<1.29.0
on bioconductor-singlecellexperiment >=1.22.0,<1.23.0
on libblas >=3.9.0,<4.0a0
on libgcc-ng >=12
on liblapack >=3.9.0,<4.0a0
on libstdcxx-ng >=12
on r-adaptgauss
on r-anocva
on r-base >=4.3,<4.4.0a0
on r-colorspace
on r-drimpute
on r-ggplot2
on r-ggpubr
on r-ggraph
on r-igraph
on r-knitr
on r-matrix
on r-mcl
on r-mixtools
on r-pheatmap
on r-polychrome
on r-rcolorbrewer
on r-rcpp >=1.0.0
on r-seurat

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-irisfgm

to add into an existing workspace instead, run:

pixi add bioconductor-irisfgm

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-irisfgm

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-irisfgm

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)