Software

FlowKit

FlowKit is an intuitive Python toolkit for flow cytometry analysis and visualization, including GatingML 2.0 support. 

SQUAC

An efficient and robust large-scale multiple testing method to infer high-dimensional gene co-expression networks based on sample-quantile contingency table.

bcSeq

A highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Bioconductor package.

capme

An efficient algorithm to estimate covariate adjusted precision matrices.

qlspack

A R package to fit mixed effect model based on quasi-least-square.

Bach

Bausch’s algorithm for chi-squared weighted sum. This software computes tail probability of a mixture of chi-squared random variables.  Implements Bausch’s algorithm using GNU GMP library so that a tail probability (or p-value) can be evaluated to an arbitrary precision. 

ELAI

Efficient Local Ancestry Inference. Software performs local ancestry inference for admixed individuals. 

hapQTL

Haplotype Quantitative Loci. This software performs association testing between local haplotypes and phenotypes at each core marker. 

piMASS

posterior inference via Model Averaging and Subset Selection. The software performs genome-wide joint analysis of all SNPs in association with a phenotype.

SCATE

An R package to extract and enhance signals from highly sparse single-cell ATAC-seq data.

TSCAN

An R package to perform pseudotime analysis for single-cell genomic data.

SCRAT

An R package to summarize regulatory activities for single-cell ATAC-seq data.

GSCA

A software tool to explore massive amounts of publicly available gene expression data.