scDD - Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

Last updated 24 days ago

immunooncologybayesianclusteringrnaseqsinglecellmultiplecomparisonvisualizationdifferentialexpression

7.88 score 32 stars 47 scripts 396 downloads

dmrseq - Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

Last updated 24 days ago

immunooncologydnamethylationepigeneticsmultiplecomparisonsoftwaresequencingdifferentialmethylationwholegenomeregressionfunctionalgenomics

5.62 score 1 packages 55 scripts 586 downloads