https://github.com/baranzinilab/kg_rag

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers

Last synced: 04 Oct 2025

https://github.com/BaranziniLab/KG_RAG

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers

Last synced: 24 Mar 2025

https://github.com/rcedgar/usearch12

Open-source usearch

bioinformatics bioinformatics-algorithms computational-biology nucleotide-alignment protein-alignment protein-sequences search-algorithms

Last synced: 14 Jun 2025

https://gregoryschwartz.github.io/too-many-cells/

Cluster single cells and analyze cell clade relationships with colorful visualizations.

bioinformatics-algorithms bioinformatics-pipeline single-cell single-cell-analysis single-cell-rna-seq visualization

Last synced: 09 Apr 2025

https://github.com/muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

bioinformatics bioinformatics-algorithms bioinformatics-tool classification dna-sequences fasta fastq genome genomic-data-analysis long-reads metagenomes metagenomic-analysis metagenomic-classification metagenomic-data metagenomics ncbi-refseq read-mapping refseq short-read-mapper taxonomy

Last synced: 09 Apr 2025

https://github.com/rcedgar/reseek

Protein structure alignment and search algorithm

bioinformatics bioinformatics-algorithms bioinformatics-tool computational-biology protein-sequences protein-structure search-algorithm

Last synced: 19 Apr 2025

https://github.com/bystrogenomics/bystro

Natural Language Search and Analysis of High Dimensional Genomic Data

bioinformatics bioinformatics-algorithms bioinformatics-analysis bioinformatics-databases bioinformatics-pipeline bioinformatics-scripts genomics genomics-search

Last synced: 17 Jan 2026

https://github.com/thejacksonlaboratory/jax-cnv

Official code repository for JAX-CNV

bioinformatics-algorithms cnv genomic ngs

Last synced: 08 Aug 2025

https://github.com/amamory/seriation

An efficient implementation of the Seriation problem which 'finds a suitable linear order for a set of objects'. It has been used to order a network of proteins such that 'related' nodes are closer in the other.

bioinformatics-algorithms protein-interaction seriation

Last synced: 18 Oct 2025

https://github.com/applicativesystem/rust-samtools-extractor

rust samtools extractor

bioinformatics-algorithms bioinofrmatics genome-alignment genome-analysis genome-bioinformatics genome-sequencing

Last synced: 15 Aug 2025

https://github.com/applicativesystem/rust-collision-algorithm

hash collision free compression of genome

bioinformatics-algorithms collision-avoidance genome-compression graphs-algorithms suffix-automaton

Last synced: 25 Aug 2025

https://github.com/ibchgenomic/suffix-arrays

rust suffix arrays

algorithms-and-data-structures bioinformatics bioinformatics-algorithms genome-analysis genome-sequencing suffix-array suffix-tree suffixarray

Last synced: 30 Mar 2025

https://github.com/ibchgenomic/collision-algorithm

hash collision free graph offset table

bioinformatics-algorithms collision-avoidance graphs-algorithms suffix-automaton

Last synced: 30 Mar 2025

https://github.com/raannakasturi/bioinfotools

BioinfoTools - A Mini Project Designed that contains most of the essential Bioinformatics Tools

bioinformatics bioinformatics-algorithms bioinformatics-tool bioinformatics-visualization biojava citations doi java jsmol

Last synced: 27 Feb 2025

https://github.com/gabywald/phylogenetik

An old Phylogenetik Project (2007) in JAVA, with (some) phylogeny, bioinformatics algorithms, matrix implementations and comparisons, PAM and BLOSUM (extract from http://gabriel.chandesris.free.fr/projets/Phylogenetik/ )

bioinformatics bioinformatics-algorithms bioinformatics-data bioinformatics-tool biology java javaswing student student-project student-work

Last synced: 29 May 2026

https://github.com/jasonjiangs/hnox_pred

HNOXPred: a web tool for the prediction of gas sensing H-NOX proteins from amino acid sequence

bioinformatics-algorithms flask javascript mysql protein-prediction python webserver

Last synced: 16 Apr 2026

https://github.com/raannakasturi/biojava

BioJava - A Mini Project Designed that contains most of the essential Bioinformatics Tools

bioinformatics bioinformatics-algorithms bioinformatics-tool bioinformatics-visualization biojava citations doi java jsmol

Last synced: 16 Apr 2026

https://github.com/applicativesystem/go-multi-longread-canvas

multipattern trimmomatic for long reads

bioinformatics bioinformatics-algorithms genome-sequencing nanopore-sequencing pacbio-hifi-sequencing-reads pacbio-sequencing

Last synced: 03 Apr 2025

https://github.com/sciencegenome/samtools-extractor

rust samtools extractor

bioinformatics-algorithms bioinofrmatics genome-alignment genome-analysis genome-bioinformatics genome-sequencing

Last synced: 18 Mar 2025

https://github.com/sciencegenome/bwt-algorithm

rust implementation of Burrows-Wheeler transform

algorithms-and-data-structures bioinformatics bioinformatics-algorithms burrows-wheeler-transformation genome-analysis genome-assembly genome-sequence-analysis

Last synced: 18 Mar 2025

https://github.com/imanghd/bioinformatics_algorithms

bioinformatics bioinformatics-algorithms python

Last synced: 05 Oct 2025

https://github.com/sciencegenome/collision-algorithm

hash collision free graph offset table

bioinformatics-algorithms collision-avoidance graphs-algorithms suffix-automaton

Last synced: 14 Jul 2025

https://github.com/gauravcodepro/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

bioinformatics-algorithms oxford-nanopore pacbio-data pacbio-sequencing sequencing variant-analysis variant-calling variants

Last synced: 19 Jul 2025

https://github.com/aayatech/knowledge-graph-llms

Knowledge Graph Generator is a Streamlit app that extracts graph data from text using LangChain and OpenAI's GPT models. 🌐 It creates interactive graphs, allowing users to visualize entities and relationships easily. 🛠️

awesome awesome-kg awsome-list bert-models bioinformatics bioinformatics-algorithms commonsense gpt4 graph graphml knowledge knowledge-base language-models large-language-models llm prompt retrieval-augmented-generation streamlit

Last synced: 26 Jun 2025

https://github.com/sciencegenome/suffix-arrays

rust suffix arrays

algorithms-and-data-structures bioinformatics bioinformatics-algorithms genome-analysis genome-sequencing suffix-array suffix-tree suffixarray

Last synced: 29 Jul 2025