GitHub topics: biological-data-analysis

Repositories

AminaHanan246/bulk_rna_seq_prj

Bulk-RNA seq workflow

Language: Python - Size: 8.86 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

samberry19/bioviper

Enhancements to Biopython for working with biological data

Language: Jupyter Notebook - Size: 9.95 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 5 - Forks: 1

SMRUCC/GCModeller

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Language: Visual Basic .NET - Size: 881 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 36 - Forks: 10

DevoLearn/devolearn

Accelerate data driven research on embryos with deep learning models :microscope:

Language: Python - Size: 409 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 49 - Forks: 30

abelew/hpgltools Fork of elsayed-lab/hpgltools

A collection of R functions to aid in host-pathogen genomic research

Language: R - Size: 529 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 5 - Forks: 1

biotoolbox/pam

Fast and Efficient Processing of PAM Data

Language: R - Size: 10.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 3 - Forks: 1

genomicssport/sequenceprofiler

rust graph and sequence profiler for reads and genomes

Language: Rust - Size: 6.57 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

kader68Biology/molecular-biology-virtual-labs

Biology Laboratory Courses

Language: Jupyter Notebook - Size: 2.45 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

michaelgruenstaeudl/BioinformaticsCourseGruenstaeudl

Coding exercises of bioinformatics course taught in fall 2023 and revised in fall 2024

Size: 54.7 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

febos/urslib2

Library for processing RNA structures using PDB, DSSR and other data

Language: Python - Size: 10.1 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 2 - Forks: 0

SmogJ/Kaggle-Competition----Stanford-Ribonanza-RNA-Folding

This project is a first look into working with Biological or Bioinformatics data and problem. This project is a naive approach to try wrangle, clean, analyze, and develop a model (ML or Neural Network) to predict RNA folding.

Language: Jupyter Notebook - Size: 7.53 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 2 - Forks: 1

sbresnahan/scAmbi

Mapping Ambiguity Overdispersion Correction for scRNA-seq

Language: HTML - Size: 1.24 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0

bbeckley-hub/BIOCHEM-BIOINFORMATICS

A smple genomic workflow for applied Bioinformaticians in Genomics and multi-omics analysis

Size: 6.84 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

rethomics/scopr

Read Ethoscope data in R

Language: R - Size: 2.5 MB - Last synced at: 21 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 6

vanvalenlab/deepcell-spots

Deep Learning Library for Spot Detection

Language: Python - Size: 211 MB - Last synced at: about 9 hours ago - Pushed at: 1 day ago - Stars: 20 - Forks: 5

hietakangas-laboratory/LAM

LAM is a quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.

Language: Python - Size: 22.9 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

pinheiroGroup/Kinbiont.jl

Ecosystem of numerical methods for microbial kinetics data analysis, from preprocessing to result interpretation.

Language: Jupyter Notebook - Size: 25 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 1

RPINerd/biox_macguffins

A loose collection of random scripts I've generated over the years

Language: Python - Size: 106 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

david-bogdan-r/ARTEM

RNA/DNA 3D structure alignment tool

Language: Python - Size: 10.5 MB - Last synced at: 2 days ago - Pushed at: 7 months ago - Stars: 3 - Forks: 0

BioJulia/BioSymbols.jl

Nucleic and amino acid primitive types

Language: Julia - Size: 2.1 MB - Last synced at: 17 days ago - Pushed at: 5 months ago - Stars: 32 - Forks: 14

chriscainx/mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Language: Python - Size: 1.05 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 74 - Forks: 33

niltonfrederico/vox-extract

VoxExtract: A Python package for extracting animal vocalization from audio files (currently Monkeys only)

Language: Python - Size: 189 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

TillMacher/TaxonTableTools

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

Language: Python - Size: 58.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 23 - Forks: 3

amckenna41/protPy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

Language: Python - Size: 255 KB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 0

pnuehrenberg/vassi

Automated scoring of social interactions in animal groups

Language: Python - Size: 54.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

AlessandroGozzoli/Hydrological-Model-Validator

Tools for the analysis and validation of Bio-Geo-Hydrological simulations and other climatological data

Language: Python - Size: 17.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

olsonjac/dna_rna_aa.py

DNA sequence Transcription and Translation tool

Language: Python - Size: 40 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

febos/SQUARNA

RNA secondary structure prediction tool

Language: Jupyter Notebook - Size: 162 MB - Last synced at: 15 days ago - Pushed at: 4 months ago - Stars: 18 - Forks: 2

digaso/pmatrix

A small script that processes data from varius csv files given some rules and outputs a excel file with all the data. This was used for a biology research.

Language: Python - Size: 2.9 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

febos/SQUARNA-data

SQUARNA benchmark data

Language: Jupyter Notebook - Size: 105 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

unmatched78/mentrual_cycle_predictor

In this project we tested various learning models for a reliable women menstraul cycle accurate prediction overtime, we have used ARISTAMA, Random forest, Long-term short memeory and many more, we used synthetic data for quick analyse

Language: Jupyter Notebook - Size: 832 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

Gitte-Hobbit/markdown

Danish biology students Rmarkdown scripts - storage and share

Size: 8.79 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

fermo-metabolomics/FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.

Language: HTML - Size: 24.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 32 - Forks: 5

abedoyaciro/analisis-nodulacion-phaseolus-rhizobium

Análisis bioestadístico de un experimento sobre la nodulación en Phaseolus vulgaris inducida por Rhizobium sp., usando R y RMarkdown para la exploración, visualización y síntesis de datos experimentales.

Language: R - Size: 1.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

rethomics/damr

Read TriKinetics' DAM data in R

Language: R - Size: 3.04 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 7

bobeobibo/phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

Language: HTML - Size: 6.8 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 52 - Forks: 15

rethomics/ggetho

Visualise high throughput behavioural data in R, based on ggplot2

Language: R - Size: 4.61 MB - Last synced at: 22 days ago - Pushed at: almost 3 years ago - Stars: 10 - Forks: 3

rethomics/behavr

Data structure to store and manipulate high throughput behavioural data in R

Language: R - Size: 8.12 MB - Last synced at: 22 days ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 4

MaxValue/Terpene-Profile-Parser-for-Cannabis-Strains

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Language: Python - Size: 21.4 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 118 - Forks: 18

opendilab/DI-bioseq

Decision Intelligence platform for Biological Sequence Searching

Language: Python - Size: 95.4 MB - Last synced at: 2 months ago - Pushed at: almost 3 years ago - Stars: 115 - Forks: 1

b-cubed-eu/euroraccoon

Generalized Additive Models (GAMs) for raccoon in Europe

Language: JavaScript - Size: 24.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

InsightSoftwareConsortium/ITKBioCell

This remote module contains classes related to segmentation of biological cells. It has classes to represent cells' shape, color, and growth state. It also has classes to represent a cell genome, whose expression is modeled by differential equations.

Language: C++ - Size: 6.61 MB - Last synced at: 10 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 4

pertzlab/ARCOS-tutorial

A Jupyter notebook to identify collective cell signalling in raw microscopy images

Language: Jupyter Notebook - Size: 7.87 MB - Last synced at: 4 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

albertruaz/Two-Species-Model

Language: Python - Size: 0 Bytes - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

mauricelanghinrichs/memocell

Bayesian inference of stochastic cellular processes with and without memory in Python.

Language: Python - Size: 55.4 MB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

XylotrupesGideon/B.-Gideon-Bergheim-public-CV

Thank you for your interest in my public CV. Feel free to contact me with any additional questions

Size: 6.41 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

bradduthie/stats

Complete introductory statistics textbook with an emphasis on the biological & environmental sciences. Includes 26 chapters introducing key concepts for a foundational understanding of statistics and 9 complementary chapters of exercises with jamovi. Supplemental shiny apps illustrate book concepts. All code and datasets are freely available.

Language: HTML - Size: 343 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 1

gletroadec/Projet_5.1

Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico Matias Rodrigues, Christian von Mering. bioRxiv 390195; doi : https://doi.org/10.1101/390195 Cependant, ces techniques reposent sur des corrélations et non sur des causalités. Elles ne permettent pas de comprendre les interactions entre organismes. Pour cela, il est important d'intégrer une autre dimension comme les informations contenues dans les réseaux métaboliques des bactéries. Pour cela, certaines bases de données existent : Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. Nature Publishing Group; 2018 Mar;36(3):272-81 https://github.com/cdanielmachado/carveme/tree/master/carveme Ce projet vise à proposer une stratégie pour détecter les interactions via les échanges de métabolites via Flux Variability Analysis. La stratégie sera a tester sur des données de microbiotes intestinales fournies par le projet HMP.

Language: Python - Size: 34.9 MB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

valtot/CounTastic

MATLAB-based software for cell counting

Language: MATLAB - Size: 50.8 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

IgnacioPachon/TFG-FTIR-ABS-R

Rsoftware - TRATAMIENTO DE DATOS QUÍMICO-FORENSES PARA LA DISCRIMINACIÓN DE FLUIDOS BIOLÓGICOS EN MATERIALES SUPERABSORBENTES

Size: 2.48 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

pylattice/pyLattice

A python library for advanced lattice light-sheet image analysis

Language: Jupyter Notebook - Size: 1.19 GB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 21 - Forks: 8

S18-Niloy/MultiFeatVotPIP Fork of ChaoruiYan019/MultiFeatVotPIP

Here, I have used Random Forest and Graph Neural Networks to classify peptide sequences into proinflammatory and non-proinflammatory categories.

Size: 878 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

ma-riviere/ShinyQPCR

Shiny app for exploring QPCR data

Language: R - Size: 1.04 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

Hat1412/Binomial-Nomenclature

The Largest Database OF Binomial Nomenclature of both plants and animals

Language: HTML - Size: 525 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 0

maxkokot/AMP-Parkinson-Baseline

A baseline solution Kagle AMP®-Parkinson's Disease Progression Prediction Competition https://www.kaggle.com/competitions/amp-parkinsons-disease-progression-prediction

Language: Jupyter Notebook - Size: 493 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

V-Z/structure-sum

Script to summarize the results from several structure runs

Language: R - Size: 28.3 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

zrkhadija/-Molecule-and-drug-Discovery-Application-For-Three-Diseases

Biomedical engineering is the application of the principles and problem-solving techniques of engineering to biology and medicine. this project aims to create Molecules and Drug discovery.

Language: Jupyter Notebook - Size: 17.7 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

hunterjsb/cellar

Advanced Microscopy Imaging Used in Medical Research

Language: Python - Size: 47.9 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

csinva/hpa-interp

Interpretations on the HPA dataset.

Language: Jupyter Notebook - Size: 6.81 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

Jas-pel/Utilitaire-ARG-NEEDLE

Cet utilitaire facilite l'utilisation d'ARG-NEEDLE en offrant des fonctionnalités supplémentaires.

Language: Python - Size: 1.09 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

SavinRazvan/heredity

An AI that assesses the likelihood of genetic traits in individuals using a Bayesian Network to analyze family genetic data, modeling genetic inheritance and mutations to infer probabilities of gene presence and trait expression.

Language: Python - Size: 3.91 KB - Last synced at: 6 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

Aniket7651/biosys-net

Bioinformatics package created in C# and python, which can analyze biological data such as DNA, RNA and protein sequences, Biological Databases Scrapping, As well as 'GEO Analysis' offers a variety of analysis on RNA-seq. Preprocessing, parsing various biological file formats (FASTA, PDB, SOFT, FASTQ, etc.), this all using C# language and dotnet.

Language: C# - Size: 6.36 MB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0