SICtools
This package is for version 3.9 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: 3.9
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("SICtools")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Using SICtools | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection |
| Version | 1.14.0 |
| 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) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SICtools_1.14.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | SICtools_1.14.0.tgz |
| 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 |
| Old Source Packages for BioC 3.9 | Source Archive |