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biocLite("Rariant")
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Rariant
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Bioconductor version: 3.0
The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.
Author: Julian Gehring, Simon Anders, Bernd Klaus (EMBL Heidelberg)
Maintainer: Julian Gehring <julian.gehring at embl.de>
Citation (from within R,
enter citation("Rariant")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Rariant")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rariant")
| HTML | R Script | Rariant |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, VariantDetection, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 3.0.2), GenomicRanges, VariantAnnotation |
| Imports | IRanges, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, methods, VGAM, dplyr, reshape2, GenomeInfoDb, S4Vectors |
| LinkingTo | |
| Suggests | h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Rariant_1.2.0.tar.gz |
| Windows Binary | Rariant_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | Rariant_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | Rariant_1.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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