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bioinformatics-algorithms

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BaranziniLab /KG_RAG

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

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

UpdatedNov 9, 2024
Jupyter Notebook

dynverse /dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

benchmarking bioinformatics-algorithms trajectory-inference

UpdatedAug 30, 2023
R

dynverse /dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

bioinformatics-algorithms single-cell-rna-seq single-cell-analysis trajectory-inference-methods trajectory-inference pseudotemporal-ordering

UpdatedDec 21, 2023
R

rcedgar /usearch12

Open-source usearch

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

UpdatedAug 19, 2025
C++

GregorySchwartz /too-many-cells

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

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

UpdatedOct 28, 2024
Haskell

imgag /ClinCNV

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

copy-number-variation bioinformatics-algorithms bioinformatics-tool

UpdatedSep 16, 2025
R

rcedgar /reseek

Protein structure alignment and search algorithm

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

UpdatedNov 5, 2025
C++

muellan /metacache

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

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

UpdatedMay 26, 2025
C++

bystrogenomics /bystro

Natural Language Search and Analysis of High Dimensional Genomic Data

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

UpdatedAug 7, 2025
Python

Bioinformatics_Algorithms

mhtjsh /Bioinformatics_Algorithms

I am sharing my code repository to understand the working and principle of working of various BioInformatics code in Python

bioinformatics bioinformatics-data bioinformatics-algorithms bioinformatics-tool

UpdatedOct 2, 2025
Python

yupenghe /REPTILE

Predicting regulatory DNA elements based on epigenomic signatures

bioinformatics dna-methylation bioinformatics-algorithms epigenomics enhancer-prediction

UpdatedJun 26, 2024
Python

njpipeorgan /L1000-bayesian

L1000 peak deconvolution based on Bayesian analysis

lincs l1000 bioinformatics-databases bioinformatics-algorithms

UpdatedOct 10, 2021
Mathematica

google /fast-simple-lcsk

Fast and simple algorithms for computing both LCSk and LCSk+

bioinformatics algorithm string strings dynamic-programming string-matching lcs bioinformatics-algorithms genome-alignment lcsk lcskpp lcskp

UpdatedMay 23, 2018
C++

Gartner-Lab /deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq

scrna-seq statistical-models bioinformatics-algorithms demultiplexing cell-hashing multi-seq

UpdatedFeb 23, 2025
R

xjtu-omics /STMiner

bioinformatics-algorithms spatial-transcriptomics

UpdatedSep 5, 2025
Python

mikeroyal /Bioinformatics-Guide

Bioinformatics Guide

python data-science awesome bioinformatics biology resources bioinformatics-pipeline bioconductor awesome-list bioinformatics-analysis bioinformatics-algorithms bioinformatics-tool

UpdatedJul 25, 2021

DatomicsGroup /deepbio

This is a curated list of tutorials, projects, libraries, videos, papers, books and anything related to applications of Deep Learning to biomedicine. Feel free to make a pull request to contribute to this list.

machine-learning bioinformatics deep-neural-networks deep-learning genomics biology computational-biology tutorials neural-networks deeplearning papers deep-learning-papers neural-nets bioinformatics-algorithms deeplearning-papers biomedicine

UpdatedSep 7, 2025

TheJacksonLaboratory /JAX-CNV

Official code repository for JAX-CNV

ngs cnv genomic bioinformatics-algorithms

UpdatedJan 16, 2020
C++

csfoo /contrafold-se

CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data

machine-learning rna-structure conditional-random-fields rna-structure-prediction bioinformatics-algorithms

UpdatedJul 11, 2024
C++

ScialdoneLab /CIARA_python

Implementation of entropy of mixing algorithm in python

opensource bioinformatics rna-seq feature-selection rna-seq-analysis bioinformatics-analysis bioinformatics-algorithms bioinformatics-tool celltype-annotation

UpdatedOct 19, 2022
Jupyter Notebook

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