https://github.com/bioconductor-source/updhmm
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: mit
- Language: R
- Default Branch: devel
- Size: 3.47 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
UPDhmm
We have developed UPDhmm R/Bioconductor package. The package provides a tool method to detect, classify and stablish the location of uniparental disomy events.
Installation
You can install the current release version of UPDhmm from Bioconductor with:
``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("UPDhmm") ```
You can install the development version of UPDhmm from GitHub with:
``` r
install.packages("devtools")
devtools::installgithub("martasevilla/UPDhmm") devtools::installgithub("martasevilla/UPDhmm") ```
Example
This is a example which show you how to solve use the package in a trio-vcf file:
r
library(UPDhmm)
library(VariantAnnotation)
file <- system.file(package = "UPDhmm", "extdata", "test_het_mat.vcf.gz")
vcf <- readVcf(file)
processedVcf <- vcfCheck(
vcf,
proband = "NA19675",
mother = "NA19678",
father = "NA19679"
)
updEvents <- calculateEvents(largecollapsed=processedVcf)
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- R >= 4.3.0 depends
- GenomicRanges * imports
- HMM * imports
- IRanges * imports
- S4Vectors * imports
- VariantAnnotation * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- dplyr * suggests
- karyoploteR * suggests
- knitr * suggests
- markdown * suggests
- regioneR * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests