toscca

Create and plot diffusion maps.

Web tool which allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box.

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests).

A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.

High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.