recipe bioconductor-findit2

find influential TF and Target based on multi-omics data

Homepage:

https://bioconductor.org/packages/3.14/bioc/html/FindIT2.html

License:

Artistic-2.0

Recipe:

/bioconductor-findit2/meta.yaml

This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.

package bioconductor-findit2

Versions:

1.0.0-0

Depends:

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicfeatures >=1.46.0,<1.47.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-multiassayexperiment >=1.20.0,<1.21.0

• bioconductor-qvalue >=2.26.0,<2.27.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-dplyr

• r-ggplot2

• r-ggrepel

• r-glmnet

• r-patchwork

• r-progress

• r-purrr

• r-rlang

• r-stringr

• r-tibble

• r-tidyr

• r-withr

Required By:

Installation

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

conda install bioconductor-findit2

and update with:

conda update bioconductor-findit2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-findit2:<tag>

(see bioconductor-findit2/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-findit2/README.html)