H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

The AnnSQL package enables SQL based queries on AnnData objects.

Build DeepSea training dataset from raw data

(current) A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Genome Contact Map Explorer - gcMapExplorer. Visit:

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Differential Privacy Protection against MembershipInference Attack on Machine Learning for Genomic Data

[G]enomic [P]ositioning with [Py]thon

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

🌳 Human ancestry inference from genomic data

PCA on Genotypes

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

Python library to query and transform genomic data from indexed files

Final Year Project Repository for correlating the personality trait with the diseases

Script to cluster Paired End Tags (PETs) from chromatin conformation capture (3C) experiments

A utility for splitting mixed origin NGS reads with secondary or alt mappings

Scripts created at CSU as a PhD student for genomic annotations and comparisons.

This repository houses the Genomic Sequence Comparison Code (GSCC), a collection of Python scripts designed for genomic sequence analysis. Whether you're comparing suspected sequences with known reference sequences or delving into bioinformatics, GSCC provides versatile tools for pairwise alignment. Feel free to explore!

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities