SICtools

DOI: 10.18129/B9.bioc.SICtools    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see SICtools.

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

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

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

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.12.0
In Bioconductor since	BioC 3.2 (R-3.2) (3.5 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SICtools_1.12.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	SICtools_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SICtools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SICtools
Package Short Url	http://bioconductor.org/packages/SICtools/
Package Downloads Report	Download Stats