recipe bioconductor-findit2

find influential TF and Target based on multi-omics data

Homepage:

https://bioconductor.org/packages/3.18/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:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-glmnet:

depends r-patchwork:

depends r-progress:

depends r-purrr:

depends r-rlang:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-withr:

requirements:

additional platforms:

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-findit2

and update with::

   mamba update bioconductor-findit2

To create a new environment, run:

mamba create --name myenvname bioconductor-findit2

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-findit2:<tag>

(see `bioconductor-findit2/tags`_ for valid values for ``<tag>``)

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