Software

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

Methylscaper optimally orders molecules (or cells) in an interactive visualization to discover methylation patterns, nucleosome positioning, and transcription factor binding sites.

Download on Bioconductor Vignette GitHub Website/Web Server

Scaffold: data-generation based simulation 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

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

Trendy is an R package that utilizes segmented regression models to simultaneously characterize each gene’s expression pattern and summarize overall dynamic activity in time-course experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. The software package also includes an R/Shiny application to view individual gene’s dynamic trends.

Download on Bioconductor Vignette GitHub

SCnorm: normalization for single-cell RNA-seq data

SCnorm is an R package that first groups genes based on their estimated count-depth relationship. Then, within each group, a quantile regression is applied to estimate scaling factors to remove the effect of sequencing depth.