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HiLDA

:package: An R package for inferring the mutational exposures difference between groups.

https://github.com/uscbiostats/hilda

Science Score: 23.0%

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Keywords

mutational-signatures r-package rjags somatic-mutations
Last synced: 9 months ago · JSON representation

Repository

:package: An R package for inferring the mutational exposures difference between groups.

Basic Info
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  • Stars: 3
  • Watchers: 1
  • Forks: 2
  • Open Issues: 1
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Topics
mutational-signatures r-package rjags somatic-mutations
Created about 7 years ago · Last pushed over 4 years ago

https://github.com/USCbiostats/HiLDA/blob/master/ 

# HiLDA: "*Hi*erarchical *L*atent *D*irichlet *A*llocation" 
[![](https://img.shields.io/badge/release%20version-1.7.5-green.svg)](https://www.bioconductor.org/packages/HiLDA) 
[![](https://img.shields.io/badge/download-2676/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/HiLDA) 
[![](https://img.shields.io/badge/doi-10.7717/peerj.7557-yellow.svg)](https://doi.org/10.7717/peerj.7557) [![](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-image-badge.svg)](https://image.usc.edu)

## Introduction

The R package `HiLDA` is developed under the Bayesian framework to allow 
statistically testing whether there is a change in the mutation burdens of 
mutation signatures between two groups. The mutation signature is defined based 
on the independent model proposed by Shiraishi's et al. 

## Paper

- **Yang Z**, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD. 2019. HiLDA: a statistical approach to investigate differences in mutational signatures. PeerJ 7:e7557 https://doi.org/10.7717/peerj.7557

## Installation 

Now you can download the pacakge from Bioconductor https://bioconductor.org/packages/devel/bioc/html/HiLDA.html

```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HiLDA")
```

## Documentation

To view documentation for the version of this package installed in your system, start R and enter:

```
browseVignettes("HiLDA")
```

## An introduction to HiLDA

Tutorials: 
https://bioconductor.org/packages/devel/bioc/vignettes/HiLDA/inst/doc/HiLDA.html

R Scripts:
https://bioconductor.org/packages/devel/bioc/vignettes/HiLDA/inst/doc/HiLDA.R

## Funding
This work was supported by NCI grant numbers 5P30 CA014089 and P01 CA196569.

Owner

  • Name: USC Division of Biostatistics
  • Login: USCbiostats
  • Kind: organization
  • Location: Los Angeles, CA

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Zhi Yang z****g@u****u 29
Nitesh Turaga n****a@g****m 8
zhiiiyang z****5@g****m 7
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Last synced: 10 months ago

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  • Average time to close pull requests: 33 minutes
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  • Average comments per issue: 8.0
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  • jennprk (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 10,381 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: HiLDA

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 10,381 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 25.0%
Downloads: 75.1%
Maintainers (1)
zyang895@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • ggplot2 * depends
  • BSgenome.Hsapiens.UCSC.hg19 * imports
  • BiocGenerics * imports
  • Biostrings * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • R2jags * imports
  • Rcpp * imports
  • S4Vectors * imports
  • TxDb.Hsapiens.UCSC.hg19.knownGene * imports
  • XVector * imports
  • abind * imports
  • cowplot * imports
  • forcats * imports
  • grDevices * imports
  • grid * imports
  • methods * imports
  • stats * imports
  • stringr * imports
  • tidyr * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests