Software

DeepDETAILS is a novel deep-learning framework that reconstructs cell-type-specific genomic signals from bulk tissue data with base-pair precision. Its core innovation is the use of readily available single-cell ATAC-seq data as a reference to deconvolve various other genomic datasets, such as those from nascent transcript sequencing or ChIP-seq.

Peak Identifier for Nascent Transcript Starts (PINTS) is a software that helps locate potential regulatory elements (promoters and enhancers) genome-wide from nascent transcript sequencing data, like GRO/PRO-cap libraries, which are specifically enriched for signals from transcription start sites (TSSs). PINTS web portal is a comprehensive catalog of promoters and enhancers, and all have support from transcriptional evidence. Besides the catalog database, the portal also allows users to upload their genomic loci of interest and analyze the loci with state-of-the-art annotations. The portal is a containerized web service powered by Django, celery, and other open-source packages.

bioSyntax is a tool designed to simplify the inspection of biological sequences, regions, and alignments. It is compatible with multiple text editors such as vim, VS Code, sublime, less, and gedit.

BioQueue is a researcher-facing platform preferentially to improve the efficiency and robustness of analysis in bioinformatics research.