Software

DLAKT

DLAKT is a Python-based toolkit for end-to-end text analysis, particularly designed for applications in social data and human-centered computational studies.

EpiScope

EpiScope is a framework for profiling epigenetic patterns and integration sites across different cell types and experimental conditions, with support for both population and single-cell resolutions.

SeqFetch

SeqFetch is a command-line utility that streamlines access to public sequencing datasets and associated metadata, delivering a unified format for analysis-ready input.

HotSpotID

HotSpotID is an algorithm designed for identifying and quantifying complex structural variants, including tandem duplications, in large-scale sequencing data.

LinkMap

LinkMap integrates multiple data sources to connect regulatory elements to their functional targets, supporting the analysis of transcriptional regulation in genomic contexts.

NetMerge

NetMerge is a scalable graph-based method for integrating proteomic and transcriptomic data to identify condition-specific biological patterns.

TextDraft

TextDraft is a collaborative scientific writing platform built around version control principles, allowing multiple users to draft, edit, and publish manuscripts programmatically.

AeroTrack

Pollution-Associated Risk Geospatial Analysis Tool (AeroTrack) is a web app and R package designed to estimate historical air quality levels across U.S. locations, supporting environmental exposure analysis for research and public health assessments.

scATAC-lab

scATAC-lab is a modular workbench for preprocessing, quality control, and analysis of single-cell chromatin accessibility datasets.

Harmoni3D

Harmoni3D is a shape analysis toolkit based on spherical harmonics, useful for modeling and comparing 3D biological structures under different conditions using statistical morphometrics.

MicroTrace

MicroTrace is a Snakemake-based pipeline for streamlined and customizable metagenomic sequencing analysis with support for plug-in extensions and modular workflows.

CellCluster+

CellCluster+ is a graph-driven suite of tools for visualizing and clustering large-scale single-cell datasets from RNA-seq and chromatin accessibility experiments.

PipeOpt

Pipeline Optimization Tool (PipeOpt) is an open-source AutoML system that uses evolutionary strategies to optimize machine learning pipelines using standard Python libraries.

CellView

CellView is a lightweight and interactive visualization platform for single-cell datasets, supporting dynamic exploration of gene expression and clustering patterns.

MetaLink

MetaLink is an R package and web-based interface that enables users to conduct various forms of meta-analysis, with tools for continuous, binary, and time-to-event outcomes, and integrated visualization and diagnostic features.