Software and programs from papers that I co-authored
Statistical Genomics and Bioinformatics
two-part-mixed-model - A Two-part Mixed Model for Differential Expression Analysis in scRNA-Seq data
intasymm - Asymmetric Integration of External Datasets to Small Local Data
rSeqRobust - Robust differential expression detection from RNA-Seq data
ELMSeq - A Unified Model for Joint Normalization and Differential Gene Expression Detection in RNA-Seq data
rSeqNP - A non-parametric approach for detecting differential expression and splicing from RNA-Seq data
rSeqDiff - Detecting differential isoform expression from RNA-seq data
rSeq - RNA-Seq Analyzer
SeqAlto - Fast and Accurate Read Alignment for Resequencing
SpliceMap - Splice Junction Discovery Using RNA-Seq
SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome
CisGenome Browser - A Compact Stand-Alone Genome Browser
CisGenome - An integrated tool for tiling array, genome and cis-regulatory element analysis, working together with CisGenome Browser
mseq - An R package for modeling non-uniformity in short-read rates in RNA-Seq data
Statistical Computing
MCMC-CE - Accurate and Efficient Calculation of Small P-Values with the Cross-Entropy Method
stcf - An Algorithm for Minimizing Sum of Truncated Convex Functions
fastPerm - An R package for quickly approximating small p-values
pslinesl1 - Fitting P-splines with an l1 penalty for repeated measures
fast-opt - Package for fast computation of the Optional Polya Tree
smooth-opt - Smoothing the OPT partition
glmnet_matlab - A matlab wrapper for glmnet, a solver for fitting Lasso (L1) and elastic-net regularized generalized linear models.