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PyTorch implementations of Generative Adversarial Networks.
Open source code for AlphaFold 2.
ChatRWKV is like ChatGPT but powered by RWKV (100% RNN) language model, and open source.
A Collection of Variational Autoencoders (VAE) in PyTorch.
arXiv LaTeX Cleaner: Easily clean the LaTeX code of your paper to submit to arXiv
Implementation and experiments of graph embedding algorithms.
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
MinHash, LSH, LSH Forest, Weighted MinHash, HyperLogLog, HyperLogLog++, LSH Ensemble and HNSW
An Open-Source Package for Network Embedding (NE)
Scripts to download genomes from the NCBI FTP servers
🧬 gget enables efficient querying of genomic reference databases
Approximate Nearest Neighbor Search for Sparse Data in Python!
A Python nearest neighbor descent for approximate nearest neighbors
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Record the CPU and memory activity of a process 📈
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
A tool for generating consensus long-read assemblies for bacterial genomes
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
A genome visualization python package for comparative genomics
Locality Sensitive Hashing using MinHash in Python/Cython to detect near duplicate text documents