recipe bioconductor-chipanalyser

ChIPanalyser: Predicting Transcription Factor Binding Sites

Homepage

https://bioconductor.org/packages/3.11/bioc/html/ChIPanalyser.html

License

GPL-3

Recipe

/bioconductor-chipanalyser/meta.yaml

Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.

package bioconductor-chipanalyser

Versions

1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

Depends

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-biocmanager

• r-rcpproll

• r-rocr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-chipanalyser

and update with:

conda update bioconductor-chipanalyser

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

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