Package: SICtools 1.35.0
Xiaobin Xing
SICtools: Find SNV/Indel differences between two bam files with near relationship
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.
Authors:
SICtools_1.35.0.tar.gz
SICtools_1.35.0.tgz(r-4.4-arm64)SICtools_1.35.0.tgz(r-4.4-x86_64)SICtools_1.35.0.tgz(r-4.3-arm64)SICtools_1.35.0.tgz(r-4.3-x86_64)
SICtools_1.35.0.tar.gz(r-4.5-noble)SICtools_1.35.0.tar.gz(r-4.4-noble)
SICtools.pdf |SICtools.html✨
SICtools/json (API)
NEWS
| # Install 'SICtools' in R: |
| install.packages('SICtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SICtools-1.35.0(bioc 3.20)SICtools-1.34.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:b1d0c2ff1e
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurldoParallelforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelambda.rlifecyclemagrittrmatrixStatsmimeopensslplyrR6RcppRhtslibrlangRsamtoolsS4VectorssnowstringistringrsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| tools for SNV/Indel Comparison between two bam files with near relationship | SICtools-package SICtools |
| main function to call indel difference between the bam files | indelDiff |
| main function to test point differences between the two bam files | snpDiff |