Open Human Genome Library

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

A multiscale pangenome browser

Whole Genome Alignment Tools

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

implicit pangenome graph

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

🌳 Create a tree using Mash distances

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

You like pytorch? You like micrograd? You love tinygrad! ❤️

Cell2Sentence: Teaching Large Language Models the Language of Biology

Application for making ENCODE Blacklists

A topic-centric list of HQ open datasets.

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The AI developer platform. Use Weights & Biases to train and fine-tune models, and manage models from experimentation to production.

Python port of the R Bioconductor `seqLogo` package

Matplotlib styles for scientific plotting

Parallel Construction of Suffix Arrays in Rust

Per-base per-nucleotide depth analysis

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

Formalizing and benchmarking open problems in single-cell genomics

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

Multi-Omics Peptide Generator

Identify and quantify MHC eluted peptides from mass spectrometry raw data

BamQuery provides RNA-seq quantification for a given peptide (from 8 to 11 residues) in chosen RNA-seq samples (single or bulk).

Protein and molecule viewer, editor, simulator

A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.

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