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: 14 Apr 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: 19 Apr 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/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: 15 Mar 2025

https://github.com/gauravcodepro/pacbio-nanopore-repeat-coverage

a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly

bioinformatics bioinformatics-algorithms bioinformatics-tool longread oxford-nanopore pacbio pacbio-sequencing sequencing-coverage sequencing-data sequencing-error

Last synced: 22 Feb 2025

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: 22 Apr 2025

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

rust samtools extractor

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

Last synced: 16 Dec 2024

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: 23 Dec 2024

https://github.com/gauravcodepro/linear-regression-model-sequence

I coded this linear regression based training model based on the sequence features across the sequences. It has two arguments, just train the model or train and predict the model

bioinformatics bioinformatics-algorithms linear-regression machine-learning machine-learning-algorithms

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/gfa-fasta

a gfa fasta write which reads the GFA alignment from the graphs and writes the fasta. modify the headers as you needs. A single excecution time with the faster iter rates.

bioinformatics bioinformatics-algorithms graphalignments graphs machinelearning pangenomes visualization

Last synced: 22 Feb 2025

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/gauravcodepro/coding-stitcher-pangenome

a coding sticher for genome annotations, which stitch all your coding regions coming out of the exon alignments and will produce the gene visualization for the pangenome

annotation-tool bioinformatics bioinformatics-algorithms genome-alignment genome-annotation protein-alignment protein-sequences

Last synced: 22 Feb 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: 22 Feb 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: 18 Mar 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/sciencegenome/collision-algorithm

hash collision free graph offset table

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

Last synced: 18 Mar 2025

https://github.com/imanghd/bioinformatics_algorithms

bioinformatics bioinformatics-algorithms python

Last synced: 28 Mar 2025

https://github.com/ndomah/bioinformatics

Bioinformatics projects and learning material

bioinformatics-algorithms database functional-genomics machine-learning molecular-biology ngs-data-analysis pipeline python r rna-seq statistics

Last synced: 04 Apr 2025

https://github.com/applicativesystem/rust-bedtools-pangenome

rust-bedtools but from the pangenome point of view.

algorithm bedtools bioinformatics bioinformatics-algorithms genome-annotation pangenome pangenome-analysis

Last synced: 24 Feb 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/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: 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/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: 27 Feb 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: 05 Mar 2025