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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SICtools")
In most cases, you don't need to download the package archive at all.
SICtools
|
This package is for version 3.4 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: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SICtools")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SICtools")
| R Script | Using SICtools | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Coverage, DataImport, QualityControl, SNP, SequenceMatching, Sequencing, Software, VariantDetection |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SICtools_1.4.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.9 (Mavericks) | SICtools_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SICtools/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/SICtools/ |
| Package Downloads Report | Download Stats |
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