grgrbu/Algorithms-in-bioinformatics

Here you can find popular algorithms in Bioinformatics, which I wrote for homework in Bioinformatics Institute (bioinf.me)

Language: Jupyter Notebook - Size: 1.63 MB - Last synced: 19 days ago - Pushed: about 3 years ago - Stars: 4 - Forks: 1

cb11711211/sc_st_attention_integration

The model and algorithm about how to implement the integration of single-cell RNA-seq and spatial transcriptomics through attention mechanism

Language: Jupyter Notebook - Size: 82.6 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

bystrogenomics/bystro

Bystro genetic analysis (annotation, filtering, statistics)

Language: Python - Size: 73 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 40 - Forks: 13

amsesk/SCGid

SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

Language: Python - Size: 11 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 3

BaranziniLab/KG_RAG

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

Language: Jupyter Notebook - Size: 9.85 MB - Last synced: 8 days ago - Pushed: 29 days ago - Stars: 342 - Forks: 49

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

Language: Python - Size: 13.7 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

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

Language: Python - Size: 28.3 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 13.7 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 159 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

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

Language: Python - Size: 18.6 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

KauanQuinzote/Bioinformatics-Algorithms

Bioinformatics Algorithms is a discipline at my university that aims to provide knowledge about manipulating DNA and RNA sequences using Python.

Language: Gnuplot - Size: 124 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

dynverse/dynbenchmark

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

Language: R - Size: 20.8 MB - Last synced: 19 days ago - Pushed: 9 months ago - Stars: 187 - Forks: 36

ScienceComputing/Python_Programming

Python codes related to medical artificial intelligence, machine learning, bioinformatics algorithms, and computer science for python programming, among others

Language: Jupyter Notebook - Size: 3.64 MB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0

GregorySchwartz/too-many-cells

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

Language: Haskell - Size: 22.3 MB - Last synced: 21 days ago - Pushed: 5 months ago - Stars: 100 - Forks: 18

SevcanDogramaci/bioinformatics-algorithms

The algorithms implemented in the extent of CENG 4217 Bioinformatics Algorithms course.

Language: Python - Size: 8.79 KB - Last synced: 26 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

dynverse/dynmethods

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

Language: R - Size: 18.9 MB - Last synced: 19 days ago - Pushed: 5 months ago - Stars: 114 - Forks: 26

Gartner-Lab/deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq

Language: R - Size: 15.9 MB - Last synced: 13 days ago - Pushed: 7 months ago - Stars: 8 - Forks: 0

yupenghe/REPTILE

Predicting regulatory DNA elements based on epigenomic signatures

Language: Python - Size: 39.7 MB - Last synced: 15 days ago - Pushed: almost 6 years ago - Stars: 28 - Forks: 4

imgag/ClinCNV

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

Language: R - Size: 48.9 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 67 - Forks: 2

mattravenhall/bio

General bioinformatics functions in Python

Language: Python - Size: 84 KB - Last synced: about 2 months ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 3

RaannaKasturi/BioinfoTools

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

Language: Java - Size: 1.42 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

RaannaKasturi/BioJava

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

Language: Java - Size: 126 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

njpipeorgan/L1000-bayesian

L1000 peak deconvolution based on Bayesian analysis

Language: Mathematica - Size: 11.8 MB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 24 - Forks: 5

muellan/metacache

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

Language: C++ - Size: 149 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 55 - Forks: 10

mikeroyal/Bioinformatics-Guide

Bioinformatics Guide

Size: 160 KB - Last synced: 1 day ago - Pushed: almost 3 years ago - Stars: 13 - Forks: 4

gaanno/Sequence-Alignment

Alineamiento bioinformático global de pares de secuencias utilizando algoritmo Needleman-Wunsch y backtracking.

Language: Python - Size: 1.95 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

kalyaniasthana/GenomeSequencing_BioinformaticsII

Coding problems from course 2 of the Bioinformatics specialization

Language: Python - Size: 42 KB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

kalyaniasthana/GenomicDataScienceAndClustering_BioinformaticsV

coding problems from course 5 of the Bioinformatics specialization

Language: Python - Size: 3.91 KB - Last synced: 5 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

kalyaniasthana/FindingMutationsInDNAAndProteins_BioinformaticsVI

coding problems from course 6 of the Bioinformatics specialization

Language: Python - Size: 185 KB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

kalyaniasthana/FindingHiddenMessagesInDNA_BioinformaticsI

Coding problems from course 1 of the Bioinformatics specialization

Language: Python - Size: 1.61 MB - Last synced: 5 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

kalyaniasthana/ncbs_coding_exercise

Language: Python - Size: 127 KB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

kalyaniasthana/ComparingGenesProteinsAndGenomes_BioinformaticsIII

coding problems from course 3 of the bioinformatics specializaton

Language: Jupyter Notebook - Size: 255 KB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 1

kalyaniasthana/MolecularEvolution_BioinformaticsIV

coding problems from course 4 of the Bioinformatics specialization

Language: Python - Size: 82 KB - Last synced: 5 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

efrenaserra/bioinformatics_algorithms

Language: Python - Size: 1000 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

aaszodi/multovl

Very fast and efficient detection of multiple overlaps between genomic regions. For details on the algorithm and the implementation, please refer to the following publication: Aszódi, A. (2012): MULTOVL: Fast multiple overlaps of genomic regions. Bioinformatics 28: 3318-3319.

Language: C++ - Size: 2.58 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 2 - Forks: 0

FatemehGholamzadeh/BWT-on-Gene-Sequence

implementation of Burrows–Wheeler transform on a Gene Sequence - Bioinformatics Course - Fall 2019

Language: Python - Size: 1.44 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

maxsalick/SGFT

Scanning gradient Fourier transform method for striated image quantification

Language: MATLAB - Size: 4.6 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

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.

Language: Python - Size: 98.6 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

csfoo/contrafold-se

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

Language: C++ - Size: 154 KB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 7 - Forks: 3

mmanoj/wildfox

Adaptive QoS and DPI platform based on mathematical models & Bioinformatics Algorithms

Size: 14.6 KB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

TheJacksonLaboratory/JAX-CNV

Official code repository for JAX-CNV

Language: C++ - Size: 2.52 MB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 10 - Forks: 2

maevemoon/hiddenmessages

Hidden Messages is an approximate 1,000 line python project using Motif Discovery, Laplace's Law of Succession, and Gibbs Sampling to identify recognisable DNA sequences within small microbial genomes, such as the oriC of E. coli.

Language: Python - Size: 55.7 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

mationai/seq-genomics

Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang

Size: 5.49 MB - Last synced: 9 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

a-fsh-r/Sharif-An-Introduction-to-Bioinformatics-Project

This repository contains my solutions for project of An Intro to Bioinformatics course held at Sharif University of Technology (SUT) by Prof. Somayyeh Koohi and Prof. Ali Sharifi Zarchi in Fall 2021, 1400-1.

Language: R - Size: 6.99 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

google/fast-simple-lcsk 📦

Fast and simple algorithms for computing both LCSk and LCSk+

Language: C++ - Size: 38.1 KB - Last synced: 8 days ago - Pushed: almost 6 years ago - Stars: 20 - Forks: 12

renatawong/bioinformatics-algorithms

Python implementation of bioinformatics algorithms and useful functions.

Language: Python - Size: 4.53 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

JasonJiangs/HNOX_Pred

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

Language: JavaScript - Size: 816 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ScialdoneLab/CIARA_python

Implementation of entropy of mixing algorithm in python

Language: Jupyter Notebook - Size: 327 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 7 - Forks: 1

luciamartinf/AssignmentAnswers

Solutions to the assignments proposed in the Bioinformatics Programming Challenges course from the Master in Computational Biology at Universidad Politécnica de Madrid.

Language: HTML - Size: 30.1 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 1

mamutalib/Bio-informatics

Bio informatics course materials for NEUB students.

Language: C++ - Size: 591 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

jeremy9959/Blog

Source for Cleverly Titled Blog

Language: SCSS - Size: 27.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

sablokgaurav/plant_single_cell_RNA_analysis

single_cell_RNA_analysis

Size: 1000 Bytes - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

fatmakahveci/Rosalind-Solutions

My solutions for rosalind problems

Language: Python - Size: 32.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

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.

Size: 87.9 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 12 - Forks: 2

PlatonB/bioinformatic-python-scripts

Простые биоинформатические скрипты на Python 3. Удобная и гибкая замена Excel/Calc для решения повседневных рутинных задач вычислительной биологии.

Language: Python - Size: 299 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 6 - Forks: 2

jaswindersingh2/SPOT-RNA-1D

RNA Backbone Torsion and Pseudotorsion Angle Prediction using Dilated Convolutional Neural Networks

Language: Python - Size: 1.86 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

mateuszstompor/Rosalind

Contains solutions to problems posted on rosalind.info

Language: Python - Size: 1.44 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jam86/Evaluation-of-a-Permutation-Based-Evolutionary-Framework-for-Lyndon-Factorizations

Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations - PPSN 2020 repository

Language: Python - Size: 1.65 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

isinaltinkaya/adv_binf_2021_week1

Teaching material used in the "Advanced Bioinformatics for Next-Generation Sequencing" class, University of Copenhagen, 2021

Language: HTML - Size: 529 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 3

titansarus/Bioinformatics-Algorithms

Answer to "Bioinformatics Algorithms" Book Coding Problems

Language: C++ - Size: 32.2 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

behdadmansouri/bioiinformatics-semi-global-alignment

Local, Semi-Global and Global Alignment for Protein Sequences

Language: Python - Size: 275 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

jithin8mathew/Bioinformatics

Python scripts for Bioinformatics applications

Language: Python - Size: 60.5 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

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.

Language: C - Size: 4.59 MB - Last synced: 12 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

celineuygun/Bioinformatics

INF103 Dönem Sonu Projesi

Language: C - Size: 193 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 2

kangjunseo/Bioinformatics

This repository is for collect python codes and jupyter notebooks when I used to solve bioinformatics problems.

Language: Jupyter Notebook - Size: 16.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

cnapy-org/optlang_enumerator

Language: Python - Size: 101 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 1

HeloiseKatharine/Alinhamento-de-sequencias-pairwise-global

Implementação do algoritmo needleman wunsch em Python

Language: Python - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

kocevaIv/bioinformatics-algorithms

Language: Python - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

rfechtner/pypairs

PyPairs - A python scRNA-Seq classifier

Language: Python - Size: 155 MB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 5

JakubMifek/mff-docs

Documents I found relevant during my studies at the faculty of Mathematics and Physics of Charles University

Language: Jupyter Notebook - Size: 40.4 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

ClarissaPereira/Finding-Ori

Identifying DnaA boxes in the origin of replication of bacterial genomes. (A repository of Python solutions to the code challenges from Unit 1 Bioinformatics Algorithms. )

Language: Python - Size: 1.64 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 2

minesh1291/BioinformaticsProjects

just a draft. Bioinformatics Projects

Size: 1.95 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

shizhuoxing/Full-Length-RNA-Toolkit

Useful tools for Full-Length RNA analysis.

Size: 17.6 KB - Last synced: 11 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

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/ )

Language: Java - Size: 1.98 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

dibaggioj/bioinformatics-rosalind

A collection of completed bioinformatics exercises from the Rosalind project and "Bioinformatics Algorithms: an Active Learning Approach" textbook by Phillip Compeau and Pavel Pevzner

Language: Python - Size: 1.82 MB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 1

rchirravurivenkata/Protein-Docking-

To identify the lowest (relatively) energy docking sites for a particular ligand using one-dimensional search.

Language: R - Size: 32.2 KB - Last synced: 4 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

PsiPhiTheta/Bioinformatics-Labs

Genome analysis scripts and laboratory files for the UofT Bioinformatics course

Language: R - Size: 7.79 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

penguin138/bioinformatics

Bioinformatics at MIPT 2018

Language: Python - Size: 18.6 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

rohitgpt178/gene_local_alignment

Language: C++ - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

Santi-7/DNA_conservation_index

This program calculates the conservation index of a set of DNA or protein sequences

Language: Python - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0