Software

methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data

Methylscaper provides an interactive and optimal ordering of individual DNA molecules to discover methylation patterns, nucleosome positioning, and transcription factor binding.

Download on Bioconductor Vignette GitHub Website/Web Server

Scaffold: data-generation simulaton of single-cell RNA-seq data

Scaffold is an R package for generating scRNA-seq data by statistically modeling each step of the experimental data generation process. Scaffold is able to simulate non-UMI, UMI, and 10X data.

GitHub Vignette

SCnorm: normalization for single-cell RNA-seq data

SCnorm first groups genes based on their estimated count-depth relationship. Within each group, a quantile regression is applied to estimate scaling factors which will remove the effect of sequencing depth.

Download on Bioconductor Vignette GitHub

Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments

Trendy utilizes segmented regression models to simultaneously characterize each gene’s expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. The top dynamic genes are then identified as genes that can be well profiled by its gene-specific segmented regression model. The software package also includes an R/Shiny application to view individual gene’s dynamic trends.