genomic-data-analysis

a framework for training sequence-level deep learning networks

A modular annotation tool for genomic variants

PANDORA 💻

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop

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

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

RADseq Data Exploration, Manipulation and Visualization using R

Phigaro is a scalable command-line tool for predicting phages and prophages

The AnnSQL package enables SQL based queries on AnnData objects.

Build DeepSea training dataset from raw data

Shiny app for making and annotating Volcano plots

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Genome Contact Map Explorer - gcMapExplorer. Visit:

(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.

genomic alignment similarity search tool

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

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

Collection of statistical scripts, image analysis workflows, data used in publications by the Misteli Lab.

An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests