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SICtools

This is the development version of SICtools; for the stable release version, see SICtools.

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


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

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

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")
Using SICtools PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection
Version 1.33.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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)
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Suggests knitr, RUnit, BiocGenerics
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Package Archives

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

Source Package SICtools_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64) SICtools_1.33.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SICtools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SICtools
Bioc Package Browser https://code.bioconductor.org/browse/SICtools/
Package Short Url https://bioconductor.org/packages/SICtools/
Package Downloads Report Download Stats