Package: SICtools
Type: Package
Title: Find SNV/Indel differences between two bam files with near
        relationship
Version: 1.42.0
Date: 2014-12-11
Author: Xiaobin Xing, Wu Wei
Maintainer: Xiaobin Xing <xiaobinxing0316@gmail.com>
Description: 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.
License: GPL (>=2)
LazyLoad: Yes
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)
Suggests: knitr, RUnit, BiocGenerics
biocViews: Alignment, Sequencing, Coverage, SequenceMatching,
        QualityControl, DataImport, Software, SNP, VariantDetection
VignetteBuilder: knitr
Packaged: 2026-06-02 22:24:27 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/SICtools
git_branch: RELEASE_3_23
git_last_commit: f10f487
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-06-02
NeedsCompilation: yes
Built: R 4.6.0; x86_64-apple-darwin20; 2026-06-03 14:36:27 UTC; unix
