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Oscope (version 1.2.0)

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

Description

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.

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Version

Version

1.2.0

License

Artistic-2.0

Maintainer

Last Published

February 15th, 2017

Functions in Oscope (1.2.0)

Run k-medoid algorithm with varying k on similarity matrix

Search for the optimal sample order for different gene clusters

Run Extended Nearest Insertion and 2-opt on a gene cluster identified by OscopeKM function

Define sine scroe cutoff using permuted data

Run the 2-opt algorithm to improve the optimal order searching of the Extended Nearest Insertion

Apply sine model on one particular gene vs. other genes

Calculate residual of polynomial fit

Search for the optimal sample order by using the Extended Nearest Insertion

OscopeExampleData

Simulated gene level data set with 600 genes and 30 cells.

Format SinFun outputs from lists to matrix

Calculate estimated mean and variance of RNA-Seq data

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

Apply sine model on the full set of genes or isoforms

Calculate absolute correlations among gene pairs

Flag gene clusters with small within-cluster phase differences and/or small within-cluster sine scores

Oscope K medoid module

Rescale the gene/isoform expression matrix

Function for searching optimal phase shift

Calculate residual of the sliding polynomial regression