Package: Oscope 1.37.0

Ning Leng

Oscope: Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.

Authors:Ning Leng

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Oscope.pdf |Oscope.html✨
Oscope/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:Oscope-1.37.0(bioc 3.21)Oscope-1.36.0(bioc 3.20)

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

immunooncologystatisticalmethodrnaseqsequencinggeneexpression

4.92 score 1 packages 14 scripts 334 downloads 11 mentions 17 exports 45 dependencies

Last updated 2 months agofrom:4ad579a3e8. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:AbsCorCalcMVFlagClusterFormatSineOutImpShiftNISFunNormForSineOpt2ShiftOscopeENIOscopeKMOscopeSinePermuCutPipeRPipeShiftCDFscanKSineFunSineOptim

Dependencies:BHBiocParallelbitopsblockmodelingbriocallrcaToolscliclustercodetoolscpp11crayondescdiffobjdigestEBSeqevaluateformatRfsfutile.loggerfutile.optionsgluegplotsgtoolsjsonliteKernSmoothlambda.rlatticelifecyclemagrittrMatrixpkgbuildpkgloadpraiseprocessxpsR6RcppRcppEigenrlangrprojrootsnowtestthatwaldowithr

Oscope_vigette

Rendered fromOscope_vignette.Rnwusingutils::Sweaveon Dec 18 2024.

Last update: 2015-07-30
Started: 2015-07-30