DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Nanopore sequence read simulator
Viral genomics analysis pipelines
A Python library for Gene–environment interaction analysis via deep learning
A package for designing compact and comprehensive capture probe sets.
Genetic learning algorithm implementation for simulations, games, or general machine learning problems
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
Efficiently keep track of changes to genomes
A tool for simulating random mutations in any genome
Understand DNA structure and how machine learning can be used to work with DNA sequence data.
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
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