I have contributed to multiple software packages for the analysis of genomic data. I am a proponent of open-source software and all packages are freely available.
slingshot | Trajectory inference methods for modeling continuous, branching processes. Designed for differentiation processes in scRNA-seq. |
tradeSeq | Spline-based (zero-inflated) negative binomial models for continuous-time expression data and clustering of temporal expression profiles. |
scry | Analysis methods for high-dimensional, small-count data. |
Dune | Consensus clustering by optimal cluster merging for improved replicability in single-cell RNA-Seq cell type discovery. |
TrajectoryUtils | Infrastructure and utilities for single-cell trajectory inference. |
condiments | Tools for analyzing trajectories across multiple conditions, including tests for differential topology, progression, and differentiation. |
traviz | A suite of functions for plotting trajectory-related objects from Bioconductor packages. It allows plotting trajectories in reduced dimensions, as well as average gene expression smoothers as a function of pseudotime. |
VDJdive | Methods for analyzing single-cell immune receptor repertoire data. It implements the E-M Algorithm for clonotype assignment, making use of ambiguous cells for improved quantification. |
cytofQC | A package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and provides associated probabilities. |
glmpca | Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed count data. |
mazing | A generative art package that provides functionality for producing, navigating, and plotting random mazes. |