bioinformatics-algorithms

There are 32 repositories under bioinformatics-algorithms topic.

BaranziniLab / KG_RAG
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
gpt knowledge-graph large-language-models llama2 llm rag retrieval-augmented-generation biomedical-applications biomedical-informatics bioinformatics gpt35turbo gpt4 llama prompt-engineering bert-models bioinformatics-algorithms context-aware knowledge-base sentence-transformers prompt-tuning
Language:Jupyter Notebook 906
dynverse / dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
benchmarking bioinformatics-algorithms trajectory-inference
Language:R 218
dynverse / dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
bioinformatics-algorithms pseudotemporal-ordering single-cell-analysis single-cell-rna-seq trajectory-inference trajectory-inference-methods
Language:R 130
rcedgar / usearch12
Open-source usearch
bioinformatics bioinformatics-algorithms computational-biology nucleotide-alignment protein-alignment protein-sequences search-algorithms
Language:C++ 121
GregorySchwartz / too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
single-cell visualization single-cell-analysis single-cell-rna-seq bioinformatics-pipeline bioinformatics-algorithms
Language:Haskell 114
imgag / ClinCNV
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
bioinformatics-tool bioinformatics-algorithms copy-number-variation
Language:R 91
rcedgar / reseek
Protein structure alignment and search algorithm
bioinformatics bioinformatics-algorithms bioinformatics-tool computational-biology protein-sequences protein-structure search-algorithm
Language:C++ 73
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 64
bystrogenomics / bystro
Natural Language Search and Analysis of High Dimensional Genomic Data
genomics genomics-search bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-databases bioinformatics-algorithms bioinformatics-scripts
Language:Python 48
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-algorithms bioinformatics-data bioinformatics-tool
Language:Python 30
yupenghe / REPTILE
Predicting regulatory DNA elements based on epigenomic signatures
enhancer-prediction bioinformatics bioinformatics-algorithms epigenomics dna-methylation
Language:Python 28
njpipeorgan / L1000-bayesian
L1000 peak deconvolution based on Bayesian analysis
bioinformatics-algorithms bioinformatics-databases l1000 lincs
Language:Mathematica 26
google / fast-simple-lcsk
Fast and simple algorithms for computing both LCSk and LCSk+
lcsk algorithm lcs string strings bioinformatics bioinformatics-algorithms dynamic-programming lcskpp lcskp string-matching genome-alignment
Language:C++ 21
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.
deep-learning deep-learning-papers genomics biomedicine bioinformatics papers tutorials bioinformatics-algorithms biology machine-learning deep-neural-networks deeplearning deeplearning-papers neural-networks neural-nets computational-biology
15
Gartner-Lab / deMULTIplex2
deMULTIplex2: robust sample demultiplexing for scRNA-seq
bioinformatics-algorithms demultiplexing scrna-seq statistical-models multi-seq cell-hashing
Language:R 15
mikeroyal / Bioinformatics-Guide
Bioinformatics Guide
bioinformatics bioinformatics-pipeline data-science bioconductor bioinformatics-algorithms bioinformatics-analysis bioinformatics-tool biology python awesome awesome-list resources
15
xjtu-omics / STMiner
bioinformatics-algorithms spatial-transcriptomics
Language:Python 15
TheJacksonLaboratory / JAX-CNV
Official code repository for JAX-CNV
cnv bioinformatics-algorithms ngs genomic
Language:C++ 13
csfoo / contrafold-se
CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data
rna-structure-prediction rna-structure conditional-random-fields machine-learning bioinformatics-algorithms
Language:C++ 9
ScialdoneLab / CIARA_python
Implementation of entropy of mixing algorithm in python
bioinformatics bioinformatics-algorithms bioinformatics-analysis bioinformatics-tool celltype-annotation feature-selection opensource rna-seq rna-seq-analysis
Language:Jupyter Notebook 9
nictru / algobio
This project aims on making the algorithms covered in the corresponding lecture at LMU Munich easier to understand by providing step-by-step logging and result visualization.
bioinformatics bioinformatics-algorithms
Language:Python 8
jaswindersingh2 / SPOT-RNA-1D
RNA Backbone Torsion and Pseudotorsion Angle Prediction using Dilated Convolutional Neural Networks
rna-torsion-angles rna-pseudotorsion-angles machine-learning convolutional-neural-networks spot-rna-1d rna-backbone-torsion angle-distributions deep-neural-networks deep-learning bioinformatics-algorithms rna-bioinformatics
Language:Python 7
mattravenhall / bio
General bioinformatics functions in Python
bioinformatics bioinformatics-algorithms genomics
Language:Python 6
PlatonB / bioinformatic-python-scripts
Простые биоинформатические скрипты на Python 3. Удобная и гибкая замена Excel/Calc для решения повседневных рутинных задач вычислительной биологии.
bioinformatic-tools bioinformatics bioinformatics-algorithms bioinformatics-pipeline bioinformatics-scripts opensource python3 vigg
Language:Python 6
grgrbu / Algorithms-in-bioinformatics
Here you can find popular algorithms in Bioinformatics, which I wrote for homework in Bioinformatics Institute (bioinf.me)
bioinformatics bioinformatics-algorithms
Language:Jupyter Notebook 5
Bioinformatics-Specialization / Bioinformatics-1
Finding Hidden Messages in DNA
bioinformatics bioinformatics-algorithms algorithms pythonprogramming
Language:Python 4
FatemehGholamzadeh / BWT-on-Gene-Sequence
implementation of Burrows–Wheeler transform on a Gene Sequence - Bioinformatics Course - Fall 2019
bioinformatics bioinformatics-analysis bioinformatics-algorithms bioinformatics-data bwt bwt-transform python python3 machine-learning machine-learning-algorithms machinelearning python-script
Language:Python 4
AdeBC / motif-finding-algorithms
Implementation of three algorithms to solve the motif finding problem.
sequence-motif bioinformatics-algorithms
Language:Python 3
amsesk / SCGid
SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries
bioinformatics-pipeline bioinformatics-algorithms bioinformatics-tool bioinformatics fungi eukaryotes single-cell-genomics genome-assembly-evaluation python3
Language:Python 3
cnapy-org / optlang_enumerator
python constraint-based-modeling bioinformatics-algorithms computational-biology stoichiometric-modeling metabolic-engineering
Language:Python 3
rfechtner / pypairs
PyPairs - A python scRNA-Seq classifier
bioinformatics bioinformatics-algorithms scrna-seq-analysis single-cell-analysis
Language:Python 3
SciComp8 / Python_Programming
Python codes related to medical artificial intelligence, machine learning, bioinformatics algorithms, and computer science for python programming, among others
artificial-intelligence bioinformatics-algorithms computer-science machine-learning python advanced basics data-structure deep-learning data-science
Language:Jupyter Notebook 3
behdadmansouri / bioiinformatics-semi-global-alignment
Local, Semi-Global and Global Alignment for Protein Sequences
bioinformatics bioinformatics-algorithms
Language:Python 2
kangjunseo / Bioinformatics
This repository is for collect python codes and jupyter notebooks when I used to solve bioinformatics problems.
rosalind rosalind-bioinformatics-challenge bioinformatics bioinformatics-algorithms python
Language:Jupyter Notebook 2
mutalibcs / Bio-informatics
Bio informatics course materials for NEUB students.
edit-distance-algorithm needleman-wunsch-algorithm neub smith-waterman-algorithm dna-transcription pdp partial-digest-problem bio-informatics bioinformatics bioinformatics-algorithms algorithm edit-distance edit-distance-algorithm-implementation edit-distance-algorithms needleman-wunsch needleman-wunsch-alignment needleman-algorithm
Language:C++ 2
titansarus / Bioinformatics-Algorithms
Answer to "Bioinformatics Algorithms" Book Coding Problems
bioinformatics bioinformatics-algorithms rosalind-solutions
Language:C++ 2

bioinformatics-algorithms

BaranziniLab / KG_RAG

dynverse / dynbenchmark

dynverse / dynmethods

rcedgar / usearch12

GregorySchwartz / too-many-cells

imgag / ClinCNV

rcedgar / reseek

muellan / metacache

bystrogenomics / bystro

mhtjsh / Bioinformatics_Algorithms

yupenghe / REPTILE

njpipeorgan / L1000-bayesian

google / fast-simple-lcsk

DatomicsGroup / deepbio

Gartner-Lab / deMULTIplex2

mikeroyal / Bioinformatics-Guide

xjtu-omics / STMiner

TheJacksonLaboratory / JAX-CNV

csfoo / contrafold-se

ScialdoneLab / CIARA_python

nictru / algobio

jaswindersingh2 / SPOT-RNA-1D

mattravenhall / bio

PlatonB / bioinformatic-python-scripts

grgrbu / Algorithms-in-bioinformatics

Bioinformatics-Specialization / Bioinformatics-1

FatemehGholamzadeh / BWT-on-Gene-Sequence

AdeBC / motif-finding-algorithms

amsesk / SCGid

cnapy-org / optlang_enumerator

rfechtner / pypairs

SciComp8 / Python_Programming

behdadmansouri / bioiinformatics-semi-global-alignment

kangjunseo / Bioinformatics

mutalibcs / Bio-informatics

titansarus / Bioinformatics-Algorithms