Software

Here is a list of software packages developed by our lab.

Bioconductor packages

  • DSS (Dispersion Shrinakge for Sequencing): differential analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq).

  • TOAST (TOols for the Analysis of heterogeneouS Tissues): designed for the analyses of high-throughput data from heterogeneous tissues that are mixtures of different cell types. TOAST offers functions for detecting cell-type specific differential expression (csDE) or differential methylation (csDM), as well as improved reference-free deconvolution for mixing proportion estimation.

  • FEAST: (FEAture SelcTion (FEAST) for Single-cell clusterin): FEAST is an R package for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.

  • POWSC: Simulation, power evaluation, and sample size recommendation for single cell RNA-seq. POWSC is a simulation-based method to provide power evaluation and sample size recommendation for single-cell RNA sequencing differential expression analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

  • PROPER (PROspective Power Evaluation for RNAseq): simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.

  • ChIPComp: Differential protein binding analysis for ChIP-seq data. The package can potentially be used for Differential analyses from other capture sequencing data with controls such as m6A capture or Ribo-seq data.
  • maanova: Differential expression analysis of N-dye microarray experiments using mixed model effect.


Other non-bioconductor software

  • Wind: weighted indexes for evaluating clustering results.

  • SC2P: two-phase differential expression for single-cell RNA-seq.

  • JAMIE: Joint Analysis of Multiple IP Experiments.

  • makeCGI: finding CpG islands (CGIs) from DNA sequences.

  • polyaPeak: ranking ChIP-seq peaks with shape information.

  • R/qtl: mapping quantitative trait loci (QTL) in experimental crosses. This package is mainly develope by Karl Broman. I helped him and wrote several core functions with C engines when I worked as a software developer at The Jackson Lab.