SICtools
Find SNV/Indel differences between two bam files with near relationship
Bioconductor version: 3.24 · Package version: 1.43.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SICtools")Details
| Maintainer | Xiaobin Xing <xiaobinxing0316@gmail.com> |
| Author | Xiaobin Xing, Wu Wei |
| License | GPL (>=2) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection |
| Package Short Url | https://bioconductor.org/packages/SICtools/ |
Citation
From within R, enter citation("SICtools"):
Xiaobin Xing, Wu Wei. SICtools: Find SNV/Indel differences between two bam files with near relationship. doi:10.18129/B9.bioc.SICtools, R package version 1.43.1, https://bioconductor.org/packages/SICtools.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SICtools_1.43.1.tar.gz |
| macOS binary (arm64) | SICtools_1.43.1.tgz |
| macOS binary (x86_64) | SICtools_1.43.1.tgz |
Dependencies
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