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https://github.com/bioconductor-source/segmenter

https://github.com/bioconductor-source/segmenter

Science Score: 13.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 41.5 MB
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  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
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Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog

README.md

Basic Checks Build and Push Docker Image

segmenter

Perform Chromatin Segmentation Analysis in R by Calling ChromHMM

Description

Call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition segmenter provides functions to test, select and visualize the output of the segmentation.

Installation

You can install the released version of segmenter from Bioconductor with:

r BiocManager::install("segmenter")

or the development version from GitHub with:

r remotes::install_github('MahShaaban/segmenter@devel')

Getting started

```r

load required libraries

library(segmenter) ```

```r

locate input and annotation files

inputdir <- system.file('extdata/SAMPLEDATA_HG18', package = 'segmenter')

coordsdir <- system.file('extdata/COORDS', package = 'chromhmmData') anchorsdir <- system.file('extdata/ANCHORFILES', package = 'chromhmmData') chromsizefile <- system.file('extdata/CHROMSIZES', 'hg18.txt', package = 'chromhmmData') ```

```r

run command

obj <- learn_model(inputdir = inputdir, coordsdir = coordsdir, anchorsdir = anchorsdir, chromsizefile = chromsizefile, numstates = 3, assembly = 'hg18', cells = c('K562', 'GM12878'), annotation = 'RefSeq', binsize = 200) ```

```r

show the object

show(obj) ```

```r

access object slots

emission(obj) ```

```r

operate on the object

get_frequency(segments = segment(obj)) ```

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

.github/workflows/basic-checks.yaml actions
  • actions/cache v1 composite
  • actions/checkout v1 composite
.github/workflows/docker-image.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v1 composite
DESCRIPTION cran
  • R >= 4.1 depends
  • ChIPseeker * imports
  • ComplexHeatmap * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • bamsignals * imports
  • chromhmmData * imports
  • graphics * imports
  • methods * imports
  • stats * imports
  • utils * imports
  • Gviz * suggests
  • TxDb.Hsapiens.UCSC.hg18.knownGene * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
inst/docker/Dockerfile docker
  • rocker/verse latest build