https://github.com/aaronwolen/bingd

bayesian integration of genomic data
https://github.com/aaronwolen/bingd

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bayesian integration of genomic data

• Host: GitHub
• URL: https://github.com/aaronwolen/bingd
• Owner: aaronwolen
• License: other
• Created: 2013-12-17T15:48:02.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2015-08-11T16:32:16.000Z (over 9 years ago)
• Last Synced: 2024-05-22T00:11:40.215Z (6 months ago)
• Language: R
• Size: 2.92 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
bingd

=====

[![Travis-CI Build Status](https://travis-ci.org/aaronwolen/bingd.png?branch=master)](https://travis-ci.org/aaronwolen/bingd)

Bayesian integration of genomic data.

Features

========

bingd assumes all features are peak ranges, represented as `GRanges` objects and saved as `RData` files. 

Feature metadata

----------------

[AnnotationHub] provides detailed metadata for each feature in its repository. bingd's `hub.metadata(online = TRUE)` function is used to retrieve the latest metadata when an internet connection is available. An extra column, `LocalPath`, is appended to the metadata, which provides the full path to a cached copy of each feature; uncached features are denoted by an `NA` in this column. If `online = FALSE` then `hub.metadata()` derived metadata from locally cached AnnotationHub features and provides only `Title` and `LocalPath`. 

Searching for features

----------------------

Genomic feature files can be searched for locally using ______ or in the AnnotationHub repository using `hub.search()`, which can be conducted online or offline.

Both functions return a list of `DataFrame`s that, at minimum, include `Title` and `LocalPath` columns.

[AnnotationHub]: http://master.bioconductor.org/packages/release/bioc/html/AnnotationHub.html