GitHub topics: biomedical-data-science

Repositories

dgidb/dgidb-v5

Providing interactions between drugs and genes sourced from a variety of publications and knowledgebases

Language: Ruby - Size: 24.5 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 24 - Forks: 4

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

Language: Python - Size: 118 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 23 - Forks: 1

MaayanLab/GeneSetCart

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

Language: TypeScript - Size: 17.7 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

Walt-Lab/waltlabtoolss

A collection of tools for biomedical research assay analysis in Python.

Language: Jupyter Notebook - Size: 7.74 MB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 3 - Forks: 3

epigen/spilterlize_integrate

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

Language: R - Size: 96.7 KB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 3

epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

Language: R - Size: 147 KB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 2

epigen/scrnaseq_processing_seurat

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

Language: R - Size: 1.27 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 22 - Forks: 0

epigen/mixscape_seurat

A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.

Language: R - Size: 113 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 19 - Forks: 2

epigen/dea_seurat

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

Language: R - Size: 358 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 21 - Forks: 11

epigen/enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

Language: Python - Size: 1.91 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 36 - Forks: 3

epigen/atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

Language: Python - Size: 46.3 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 53 - Forks: 2

maxkayser/ectmetrics

A Python Library for Calculating Seizure Quality Indices in Electroconvulsive Therapy

Language: Python - Size: 2.04 MB - Last synced at: 10 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 1

epigen/rnaseq_pipeline

RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

Language: Python - Size: 60.5 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 2 - Forks: 0

NIH-NEI/SCassist

SCassist : An AI Based Workflow Assistant for Single-Cell Analysis

Language: R - Size: 24.2 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 3 - Forks: 2

YuxingLu613/awesome-biomedical-knowledge-graphs

A curated list of Biomedical Knowledge Graph related learning materials, databases, tools and other resources

Size: 22.5 KB - Last synced at: 11 days ago - Pushed at: 8 months ago - Stars: 13 - Forks: 1

pscedu/singularity

Just a list of Singularity definition files maintained by the Biomed Applications Group

Language: Python - Size: 182 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

Alliance-RDM-GDR/RDM_BioimageFAIR

[EN] This repository contains a presentation for sharing biomedical images and reproducible workflows into generalist repositories like FRDR. [FR] Ce dépôt contient une présentation pour le partage d'images biomédicales et de flux de travail reproductibles dans des dépôts généralistes comme DFDR.

Language: HTML - Size: 14.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

arturomoncadatorres/breathing-rate-rsa

Implementation of the methods used to calculate (average) respiratory rate from heart rate variability as shown in the paper by Schafer and Kratky (2008).

Language: Jupyter Notebook - Size: 10.4 MB - Last synced at: 14 days ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 1

tinykishore/playground

Playground: A Personal Sandbox for Code and Curiosity

Language: Jupyter Notebook - Size: 15.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

LengerichLab/CompBioDatasetsForMachineLearning

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Size: 43.9 KB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 171 - Forks: 25

robert-haas/kgw

Knowledge graph workflows with Python.

Language: Python - Size: 1.21 MB - Last synced at: 8 days ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

aangelopoulos/im2im-uq

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

Language: Python - Size: 5.24 MB - Last synced at: 8 days ago - Pushed at: about 2 years ago - Stars: 55 - Forks: 9

BorgwardtLab/S3M

A software package for statistically significant shapelet mining

Language: C++ - Size: 2.88 MB - Last synced at: 16 days ago - Pushed at: over 2 years ago - Stars: 53 - Forks: 8

AnthonyMRios/adversarial-relation-classification

Unsupervised domain adaptation method for relation extraction

Language: Python - Size: 17.6 KB - Last synced at: 16 days ago - Pushed at: almost 7 years ago - Stars: 18 - Forks: 9

carpentries-incubator/fair-for-busy-biologists

A short course on FAIR and data managment for biomedical research

Size: 49.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 0

Spandan2308/Protein-Protein-Interaction-Prediction

Sequence based PPI prediction algorithm is developed using Xgboost. Around 73,000 positive and negative interacting protein pairs were extracted from Pan’s PPI dataset

Language: Jupyter Notebook - Size: 82.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

azminewasi/CADGL

Data and code of CADGL: Context-Aware Deep Graph Learning for Predicting Drug-Drug Interactions

Language: Python - Size: 6.46 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

hms-dbmi/EHRtemporalVariability

R package for delineating temporal dataset shifts in Eletronic Health Records

Language: HTML - Size: 11.7 MB - Last synced at: 13 days ago - Pushed at: 12 months ago - Stars: 17 - Forks: 8

StatBiomed/BMDS-book

Biomedical Data Science book

Language: HTML - Size: 12.5 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 3

jvwilliams23/pyssam

A Python library for biomedical statistical shape and appearance modelling.

Language: Python - Size: 28.4 MB - Last synced at: 30 days ago - Pushed at: 10 months ago - Stars: 30 - Forks: 3

Sorelz/Kaggle_MSK

Project for Kaggle competition on spotting cancer by NLP - coworking with Rafi Zonenashvili

Language: Jupyter Notebook - Size: 880 MB - Last synced at: 5 months ago - Pushed at: about 7 years ago - Stars: 4 - Forks: 1

SUGAM2001/Feature-Selection-Techniques-in-EEG

Feature selection methods for EEG data analysis.

Language: Python - Size: 14.6 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

bioshot-dotcom/BMI_weight_prediction

This project is part of the Machine Learning Project course at UCL Louvain University, conducted during the academic year 2021/2022.

Language: Jupyter Notebook - Size: 377 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

ydavidchen/hrd_tnbc

Bioinformatic, statistical & ML analysis of Homologous Recombination Deficiency in triple-negative breast cancer

Language: R - Size: 68.4 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

amarrammadhu/Biomedical-Engineering-

My assignments and projects concerned with Biomedical Engineering

Language: TeX - Size: 5.26 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

pwatrick/ddiwas

Language: R - Size: 4.64 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

m89p067/equiv_med

Functions for clinical equivalence testing

Language: Python - Size: 813 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

SisonkeBiotik-Africa/MeSH2Matrix

A set of Python codes for the classification of biomedical relations based on the MeSH keywords of PubMed scholarly publications

Language: Jupyter Notebook - Size: 4.86 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 6 - Forks: 0

gbatsis/heart-failure-predictor

This repository contains a web application designed to predict the likelihood of heart disease in patients using machine learning models.

Language: Jupyter Notebook - Size: 7.57 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

The-Lammert-Lab/tinnitus-reconstruction

Reconstruct high-dimensional spectral representations of tinnitus using reverse correlation

Language: MATLAB - Size: 40.2 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 2

ncbi-nlp/PubMed-Best-Match

Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches

Language: Python - Size: 2.63 MB - Last synced at: 11 months ago - Pushed at: almost 7 years ago - Stars: 38 - Forks: 11

gnlca/heart-failure-detection

Heart Failure Detection with Deep Learning project for the University Course 'Biomedical Data Management and Analysis'.

Language: Jupyter Notebook - Size: 4.46 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

JJSanabriaS/1996_now_other_AI-image_processing_projects

compilation for different projects code in python, c++. visual basic, matlab, labview, java,html

Language: Python - Size: 16.6 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

JJSanabriaS/2022-head_movement_-sample-

Mechanical, electrical and control system for disabled people assistance code on arduino (ç++)

Language: C++ - Size: 469 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

JJSanabriaS/2022_nutri_-sample-

web based Non linear optimization for health assistance code on php

Language: PHP - Size: 17.6 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

tim-peterson/R-graphing-statistics

An example for biomedical scientists of how to do statistics and graphing of groups of data.

Size: 177 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

tanmaybasu/Qualitative-Text-Analysis-of-Healthcare-Data-Using-NLP

A text summarization framework to identify major opinions from healthcare text

Language: Python - Size: 46.9 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 0

mper162/Infant-muscle-data-processing-

Engaged in processing infant MRI data, primarily concentrating on crafting scripts to quantify muscle volume and length in the lower limbs.

Language: MATLAB - Size: 11.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

i6092467/pediatric-appendicitis-ml

Using ML to predict the diagnosis, management, and severity of pediatric appendicitis

Language: R - Size: 194 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 1

premDelaprem/MRI-tumor-classification

Building CNN models to detect and classify brain tumors using images of MRI scans

Language: Jupyter Notebook - Size: 26.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

pscedu/apptainer

Just a list of Apptainer definition files maintained by the Biomed Applications Group

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

YeshwanthZ/BDS_usingR

2 Projects on Biomedical Data Science

Size: 21.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

bio-ontology-research-group/opa2vec

Turning Ontologies Plus Annotation Properties into Vectors

Language: Groovy - Size: 17.2 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 34 - Forks: 10

mida-project/meta Fork of MIMBCD-UI/meta

:paperclip: About MIDA Project

Size: 143 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 12 - Forks: 1

FAIRplus/Data-Maturity

FAIR Dataset Maturity model

Language: SCSS - Size: 22.8 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 10

gaoyuanliang/deep_depression_detector

Deep learning model of depression detection from activity sensor data

Language: Python - Size: 1.78 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 12 - Forks: 1

charlesli37/covid-oph-dx-utils

Online content for "Shifts in ophthalmic care utilization during the COVID-19 pandemic in the United States"

Size: 5.89 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

rcv911/spectrum-average

EEG spectrum mean of 84 records

Language: Python - Size: 94.7 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1

rcv911/coherence-function

Language: Python - Size: 506 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1

rcv911/periodogram

Draw periodogram of real EEG data

Language: Python - Size: 1.8 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 2

Mina-Moeini/BioMedical-Segmentation

Language: Jupyter Notebook - Size: 2.55 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

BrianaB2206/Estimation-of-patient-survival-chances_ICU_Diploma_Project

The project aimed to implement a digital processing algorithm of biomedical signals to estimate the chances of survival for patients admitted to the ICU. A classification model based on artificial intelligence was implemented to estimate the chances of survival.

Language: Jupyter Notebook - Size: 41 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

muq2002/motor_imaginary_bci

This dome project to classify brain imaginary movement

Language: MATLAB - Size: 236 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

bertpt/u-net

Segmentation of Biomedical Images is based on U-Net. This U-Net implementation using Keras and TensorFlow has varying depth that can be specified by model input.

Language: Python - Size: 453 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 2

shreyaspadhy/UNet-Zoo

A collection of UNet and hybrid architectures in PyTorch for 2D and 3D Biomedical Image segmentation

Language: Python - Size: 786 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 356 - Forks: 78

awcasella/Template-TCC-LaTeX-UNIFESP-SJC-EngBio

Template LaTeX de TCC Engenharia Biomédica da UNIFESP-SJC.

Language: TeX - Size: 637 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

awcasella/Calculo-Numerico-UNIFESP-SJC-EngBio

This repository contains all the algorithms studied in discipline "Calculo Numerico" of Biomedical Engineering course at UNIFESP in the second semester of 2018.

Language: MATLAB - Size: 22.5 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 1

awcasella/Engenharia-Medica-Aplicada-UNIFESP-SJC-EngBio

This repository contains all the machine learning algorithms studied in discipline "Engenharia Médica Aplicada" of Biomedical Engineering course at UNIFESP in the second semester of 2018. All the algorithms are written in both MatLab and Python Languages.

Language: MATLAB - Size: 102 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

rbr7/DREAM_challenge-COVID-19_EHR

DREAM challenge 2021 - To facilitate understanding risk factors that lead to a positive COVID-19 test utilizing electronic health recorded data mapped to the OMOP Common Data Model. UW Medicine clinical data sets also used. Submission for challenge part Q2.

Language: Jupyter Notebook - Size: 25.7 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0