Package: RTIGER 2.1.0

RTIGER: HMM-Based Model for Genotyping and Cross-Over Identification

Our method integrates information from all sequenced samples, thus avoiding loss of alleles due to low coverage. Moreover, it increases the statistical power to uncover sequencing or alignment errors <doi:10.1093/plphys/kiad191>.

Authors:Rafael Campos-Martin [cre], Sophia Schmickler [aut], Manish Goel [ctb], Korbinian Schneeberger [aut], Achim Tresch [aut]

RTIGER_2.1.0.tar.gz
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RTIGER_2.1.0.tar.gz(r-4.5-noble)RTIGER_2.1.0.tar.gz(r-4.4-noble)
RTIGER_2.1.0.tgz(r-4.4-emscripten)RTIGER_2.1.0.tgz(r-4.3-emscripten)
RTIGER.pdf |RTIGER.html✨
RTIGER/json (API)

# Install 'RTIGER' in R:
install.packages('RTIGER', repos = c('https://rfael0cm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rfael0cm/rtiger/issues

Datasets:
  • ATseqlengths - The autosome chromosome lengths for Arabidopsis Thaliana.
  • myDat - A fitted example using three own samples of Arabidopsis. More information in publication:

On CRAN:

Conda:

genomeannotationhiddenmarkovmodelsequencing

4.30 score 4 stars 5 scripts 164 downloads 9 exports 66 dependencies

Last updated 1 years agofrom:c187e84113. Checks:1 OK, 8 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-winERRORMar 24 2025
R-4.5-macERRORMar 24 2025
R-4.5-linuxERRORMar 24 2025
R-4.4-winERRORMar 24 2025
R-4.4-macERRORMar 24 2025
R-4.4-linuxERRORMar 24 2025
R-4.3-winERRORMar 24 2025
R-4.3-macERRORMar 24 2025

Exports:calcCOnumberdevfitgenerateObjectoptimize_RplotCOsRTIGERsetupJuliasourceJulia

Dependencies:askpassBiobaseBiocGenericsclasscliclustercolorspacecurle1071evaluateextraDistrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhttrIRangesisobandjsonliteJuliaCallknitrlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeoompaBaseoompaDataopensslpillarpkgconfigplyrproxyqpdfR6RColorBrewerRcppreshape2rjsonrlangS4VectorsscalesstringistringrsysTailRanktibbleUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryaml

A quick guide to crossover identification using RTIGER

Rendered fromtutorial_RTIGER.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2023-03-25
Started: 2021-03-27