To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SICtools")

In most cases, you don't need to download the package archive at all.

SICtools

 

   

Find SNV/Indel differences between two bam files with near relationship

Bioconductor version: Release (3.5)

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

Author: Xiaobin Xing, Wu Wei

Maintainer: Xiaobin Xing <xiaobinxing0316 at gmail.com>

Citation (from within R, enter citation("SICtools")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SICtools")

Documentation

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

browseVignettes("SICtools")

 

PDF R Script Using SICtools
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection
Version 1.6.0
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License GPL (>=2)
Depends R (>= 3.0.0), methods, Rsamtools(>= 1.18.1), doParallel (>= 1.0.8), Biostrings(>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges(>= 1.22.4), IRanges(>= 2.4.8)
Imports
LinkingTo
Suggests knitr, RUnit, BiocGenerics
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 SICtools_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) SICtools_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SICtools/tree/release-3.5
Package Short Url http://bioconductor.org/packages/SICtools/
Package Downloads Report Download Stats

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