Transfer HiFi read mappings from their own assembly contigs to a standard reference

genotype and visualize structural variants in the human pangenome graphs

an API for intersections of genomic data

A cat(1) clone with wings.

A tool for sniffing out the differences in vari-Ants

Hone computational biology skills by re-enacting Figure 1 of modern biology papers

Scalable genetics toolkit

Ultrafast GPU-enabled QTL mapper

🧬 High-performance VCF file parser and reformatter with VEP annotation support. Converts complex VCF files to analyzable TSV format with intelligent transcript handling.

Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

strange cross-platform, performance-oriented and interactive pangenome and large graph visualization

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A complete diploid human genome

Tool for the Quality Control of Long-Read Defined Transcriptomes

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

long read RNA-seq quantification

LongcallR is a SNP caller for single molecule long-read RNA-seq data

A local-haplotagging-based small and structural variant caller

Easy genomic regions for short-read variant calling

k-mer learning materials

Joint structural variant and copy number variant caller for HiFi sequencing data

Feature-rich Python implementation of the tximport package for gene count estimation.

A genome browser designed for complex structural variants and long reads.

Implement a ChatGPT-like LLM in PyTorch from scratch, step by step

Getting Started with PyTorch Lightning, Published by Packt

Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.