dnbaker / bioseq
Tokenizers and Machine Learning Models for biological sequence data
☆25Updated 6 months ago
Alternatives and similar repositories for bioseq:
Users that are interested in bioseq are comparing it to the libraries listed below
- Plot multiple sequence alignment (MSA)☆14Updated 7 months ago
- Learning to untangle genome assembly with graph neural networks.☆72Updated 5 months ago
- A lightweight platform-accelerated library for biological motif scanning using position weight matrices.☆44Updated last month
- Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!☆23Updated last month
- Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.☆72Updated 2 weeks ago
- Diverse Genomic Embedding Benchmark☆45Updated last month
- A genome browser in your Jupyter notebook☆31Updated 4 months ago
- A Generative Pre-Trained Transformer Package for Pangenomes☆50Updated 11 months ago
- Bidirectional WFA (Paper)☆46Updated 11 months ago
- Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.☆20Updated 11 months ago
- Prediction of virus-host association using protein language models and multiple instance learning☆17Updated 10 months ago
- Machine learning methods for DNA sequence analysis.☆41Updated last week
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆17Updated 3 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆28Updated 3 weeks ago
- Intel lab's open sourced data science framework for accelerating digital biology☆47Updated last week
- toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files☆22Updated 8 months ago
- ☆32Updated 8 months ago
- Fast, sensitive and accurate protein remote homology search on GPUs☆15Updated 11 months ago
- SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.☆16Updated 3 years ago
- Deep learning embedding for nucleotide sequences☆18Updated 3 weeks ago
- ☆9Updated 10 months ago
- ✂️ Deep learning-based splice site predictor that improves spliced alignments☆51Updated last month
- Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…☆61Updated 3 months ago
- GRAph-based Finding of Individual Motif Occurrences☆31Updated 7 months ago
- Universal and efficient core gene phylogeny with Foldseek and ProstT5☆55Updated 2 weeks ago
- A python library for creating simulated regulatory DNA sequences☆38Updated 2 years ago
- MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect☆27Updated 2 weeks ago
- A tool for summarizing, extracting, generating and modifying DNA sequences.☆23Updated 4 months ago
- Detecting Sequence Signals in Targeting Peptides Using Deep Learning☆12Updated 5 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 10 months ago