Package Recipe 'bioconductor-singlemoleculefootprinting'

recipe bioconductor-singlemoleculefootprinting

Analysis tools for Single Molecule Footprinting (SMF) data

Homepage:: https://bioconductor.org/packages/3.16/bioc/html/SingleMoleculeFootprinting.html
License:: GPL-3
Recipe:: /bioconductor-singlemoleculefootprinting/meta.yaml

SingleMoleculeFootprinting is an R package providing functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location

package bioconductor-singlemoleculefootprinting¶

Versions:

1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

bioconductor-biocgenerics >=0.44.0,<0.45.0
bioconductor-biostrings >=2.66.0,<2.67.0
bioconductor-bsgenome >=1.66.0,<1.67.0
bioconductor-genomeinfodb >=1.34.0,<1.35.0
bioconductor-genomicranges >=1.50.0,<1.51.0
bioconductor-iranges >=2.32.0,<2.33.0
bioconductor-quasr >=1.38.0,<1.39.0
r-base >=4.2,<4.3.0a0
r-data.table
r-plyr
r-rcolorbrewer

Required By:

Installation

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

conda install bioconductor-singlemoleculefootprinting

and update with:

conda update bioconductor-singlemoleculefootprinting

or use the docker container:

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

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