Package: localScore 1.0.11

David Robelin

localScore: Package for Sequence Analysis by Local Score

Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).

Authors:Sebastian Simon [aut], David Robelin [aut, cre], Sabine Mercier [aut], Sebastien Dejean [aut], The authors of Eigen the library for the included version of Eigen [cph]

localScore_1.0.11.tar.gz
localScore_1.0.11.tar.gz(r-4.5-noble)localScore_1.0.11.tar.gz(r-4.4-noble)
localScore_1.0.11.tgz(r-4.4-emscripten)localScore_1.0.11.tgz(r-4.3-emscripten)
localScore.pdf |localScore.html✨
localScore/json (API)

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.00 score 4 scripts 187 downloads 23 exports 1 dependencies

Last updated 1 years agofrom:b8b2fea6b1. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-linux-x86_64OKDec 03 2024

Exports:automatic_analysisCharSequence2ScoreSequenceCharSequences2ScoreSequencesdaudinexact_mckarlinkarlinMonteCarlokarlinMonteCarlo_doublelindleyloadMatrixFromFileloadScoreFromFilelocalScoreClocalScoreC_doublemaxPartialSumdmccmonteCarlomonteCarlo_doubleRealScores2IntegerScoresscoreDictionnary2probabilityVectorscoreSequences2probabilityVectorsequences2transmatrixstationary_distributiontransmatrix2sequence

Dependencies:Rcpp

Local Score Package

Rendered fromlocalScorePackageDocumentation.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2023-11-02
Started: 2021-02-23

Readme and manuals

Help Manual

Help pageTopics
Package for sequence analysis by local scorelocalScore-package localScore
Congenital oesophageal atresia dataAeso
Deprecated. Use 'Aeso' instead.aeso.data
Automatic analysisautomatic_analysis
Convert a character sequence into a score sequenceCharSequence2ScoreSequence
Convert several character sequences into score sequencesCharSequences2ScoreSequences
Daudin [p-value] [iid]daudin
Deprecated. Use 'HydroScore' instead.dico
Exact method for p-value [Markov chains]exact_mc
DictionnaireHydroScore
Karlin [p-value] [iid]karlin
Monte Carlo - Karlin [p-value]karlinMonteCarlo
Monte Carlo - Karlin for real scores[p-value]karlinMonteCarlo_double
Lindley processlindley
Loads matrix from csv-FileloadMatrixFromFile
Load score from fileloadScoreFromFile
Local scorelocalScoreC
Local score for sequences of floating valueslocalScoreC_double
Deprecated. Use 'Seq1093' instead.LongSeq
Maximum of the partial sum [probability] [iid]maxPartialSumd
MCC [p-value] [iid]mcc
Deprecated. Use 'Seq219' instead.MidSeq
Monte Carlo method [p-value]monteCarlo
Monte Carlo method for real score case [p-value]monteCarlo_double
Deprecated. Use 'SeqListSCOPe' instead.MySeqList
Convert a real scores vector into an integer scores vectorRealScores2IntegerScores
Check for missing scores values in the score distributionscoreDictionnary2probabilityVector
Empirical distribution from sequencesscoreSequences2probabilityVector
Long protein sequenceSeq1093
Protein sequenceSeq219
Short protein sequenceSeq31
Several sequencesSeqListSCOPe
Transition matrix from sequence(s)sequences2transmatrix
Deprecated. Use 'Seq31' instead.ShortSeq
Stevens-Johnson syndrome dataSJSyndrome.data
Stationary distribution [Markov chains]stationary_distribution
Sampling function for Markov chainstransmatrix2sequence