biomedical-data-science

There are 36 repositories under biomedical-data-science topic.

shreyaspadhy / UNet-Zoo
A collection of UNet and hybrid architectures in PyTorch for 2D and 3D Biomedical Image segmentation
unet deep-learning biomedical-data-science imagesegmentation rnn cnn pytorch lstm bdclstm kunet
Language:Python 363
LengerichLab / CompBioDatasetsForMachineLearning
A Curated List of Computational Biology Datasets Suitable for Machine Learning
datasets curated-list machine-learning computational-biology dataset computational-biology-datasets biomedical-data-science
157
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.
unet uncertainty uncertainty-quantification uncertainty-estimation quantile-regression image-to-image-translation biomedical-image-processing biomedical-data-science computational-biology computational-imaging mri machine-learning microscopy pytorch
Language:Python 52
BorgwardtLab / S3M
A software package for statistically significant shapelet mining
time-series time-series-analysis time-series-analysis-tool significant-pattern-mining shapelets biomedical-data-science biomedical
Language:C++ 52
Beknaizer / OCT-Retinal-Layer-Segmenter
UNet based model that segment retina to 8 layers in OCT images
biomedical-data-science biomedical-image-processing computer-vision-algorithms deep-learning deep-neural-networks image-segmentation images keras-tensorflow machine-learning neural-networks python retinal-layer-segmentation segmentation
Language:Jupyter Notebook 49
epigen / atacseq_pipeline
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
snakemake atac-seq python bioinformatics workflow ngs pipeline biomedical-data-science bash
Language:Python 47
ncbi-nlp / PubMed-Best-Match
Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches
machine-learning text-mining feature-engineering biomedical-data-science
Language:Python 40
PingjunChen / GradingKneeOA
Knee Osteoarthritis Analysis with X-ray Images using CNN
deep-learning biomedical-data-science knee-joints knee-osteoarthritis-analysis kl-grading grading-system x-ray-images cnn-classification yolov2
Language:Python 38
bio-ontology-research-group / opa2vec
Turning Ontologies Plus Annotation Properties into Vectors
ontology machine-learning artificial-intelligence biomedical-data-science
Language:Groovy 35
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.
bioinformatics genomic-regions enrichment-analysis atac-seq biomedical-data-science chip-seq gene-set-enrichment gene-sets rna-seq visualization pipeline snakemake workflow motif-enrichment-analysis
Language:Python 32
jvwilliams23 / pyssam
A Python library for biomedical statistical shape and appearance modelling.
biomedical-data-science biomedical-image-processing python statistical-shape-model
Language:Python 30
hisunjiang / Public-datasets-of-BCI
Popular public datasets of BCI
bci eeg biomedical-data-science
25
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.
atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom rna-seq snakemake visualization volcano-plot workflow scrna-seq statistics r
Language:R 23
verifAI
nikolamilosevic86 / verifAI
VerifAI initiative to build open-source easy-to-deploy generative question-answering engine that can reference and verify answers for correctness (using posteriori model)
biomedical-data-science machine-learning natural-language-processing nlp nlp-machine-learning bioasq deep-learning llm medline mistral-7b nli pubmed qlora scifact verification hallucination-detection openai opensearch qdrant
Language:Jupyter Notebook 21
AnthonyMRios / adversarial-relation-classification
Unsupervised domain adaptation method for relation extraction
machine-learning biomedical-data-science bioinformatics relation-extraction natural-language-processing nlp nlp-machine-learning
Language:Python 19
epigen / genome_tracks
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.
atac-seq bioinformatics pipeline python rna-seq snakemake visualization workflow biomedical-data-science genomic-regions genome-browser genome-track scrna-seq
Language:Python 19
dgidb / dgidb-v5
Providing interactions between drugs and genes sourced from a variety of publications and knowledgebases
bioinformatics biomedical-data-science genomics drug-target-interactions
Language:Ruby 18
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.
bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization workflow volcano-plot
Language:R 16
hms-dbmi / EHRtemporalVariability
R package for delineating temporal dataset shifts in Eletronic Health Records
dataset-shifts time electronic-health-records visualization data-quality data-quality-monitoring biomedical-data-science biomedical-informatics variability
Language:HTML 16
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.
bioinformatics workflow snakemake scrna-seq biomedical-data-science cite-seq sccrispr-seq 10xgenomics snrna-seq single-cell visualization
Language:R 15
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.
bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow
Language:R 14
epigen / spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
atac-seq batch-effect chip-seq count-matrix dimensionality-reduction integration ngs normalization rna-seq bioinformatics biomedical-data-science pipeline snakemake visualization workflow
Language:Python 14
deep_depression_detector
gaoyuanliang / deep_depression_detector
Deep learning model of depression detection from activity sensor data
deep-learning depression depressed keras tensorflow cnn signal-processing biomedical-data-science mental-health mental-health-awareness mental-disorder
Language:Python 13
meta
mida-project / meta
:paperclip: About MIDA Project
human-computer-interaction user-interface user-experience user-centered-design health-informatics biomedical biomedical-image-processing biomedical-informatics biomedical-engineering biomedical-data-science medical-imaging medical-image-processing deep-learning deep-neural-networks deep-reinforcement-learning machine-learning assistant medical-assistant cancer-research cancer-imaging-research
13
jakelever / knowledgediscovery
Analysis code for knowledge discovery project
knowledge-discovery data-science big-data biomedical-data-science literature-mining
Language:Python 12
bccummings / acq-tools
Toolkit for analyzing physiologic data collected via Biopac AcqKnowledge software.
biopac data-acquisition research-data-management physiology health-informatics biomedical-data-science biomedical-engineering
Language:Python 11
ushukkla / Test-The-Tongue
It is a Bio-Medical Image based project, where we are testing the diseases through tongue image scanning.
biomedical-data-science medical-imaging medical-image-processing deep-neural-networks python3 matlab-script matlab-image-processing-toolbox image-processing computer-vision
Language:MATLAB 10
FAIRplus / Data-Maturity
FAIR Dataset Maturity model
biomedical-data-science lifescience fair fair-data maturity-model
Language:SCSS 9
i6092467 / pediatric-appendicitis-ml
Using ML to predict the diagnosis, management, and severity of pediatric appendicitis
machine-learning classification decision-support-systems biomedical-data-science medical-informatics
Language:R 9
YuxingLu613 / awesome-biomedical-knowledge-graphs
A curated list of Biomedical Knowledge Graph related learning materials, databases, tools and other resources
bioinformatics biomedical-data-science knowledge-graph largelanguagemodel
8
victorvicpal / biofes
Biomedical Feature Selection for Machine Learning Models
machine-learning inferential-statistics multivariate-statistics biomedical-data-science
Language:Python 7
SisonkeBiotik-Africa / MeSH2Matrix
A set of Python codes for the classification of biomedical relations based on the MeSH keywords of PubMed scholarly publications
biomedical-data-science dataset deep-learning machine-learning ontology-engineering relation-classification
Language:Jupyter Notebook 6
StatBiomed / BMDS-book
Biomedical Data Science book
biomedical-data-science case-studies r-programming
Language:HTML 6
covid19sdtool
carsaesi / covid19sdtool
R code for the discovery of COVID-19 subgroups by symptoms and comorbidities.
covid-19 covid19 subgroup-discovery subgroup-analysis data-quality heterogeneity variability frailty biomedical-informatics biomedical-data-science
Language:HTML 5
fredhutchio / coding_for_cancer
An introduction to computational thinking and performing biomedical research with R for high school students
training highschool biomedical biomedical-data-science education computational-biology computational-thinking
5
Taneja24 / Semantic-Segmentation-of-Microscopy-Cell-Images
Identify microscopy cells in biomedical images using semantic segmenting with U-Net Architecture
healthcare semantic-segmentation artificial-intelligence u-net biomedical-data-science
Language:Jupyter Notebook 5

biomedical-data-science

shreyaspadhy / UNet-Zoo

LengerichLab / CompBioDatasetsForMachineLearning

aangelopoulos / im2im-uq

BorgwardtLab / S3M

Beknaizer / OCT-Retinal-Layer-Segmenter

epigen / atacseq_pipeline

ncbi-nlp / PubMed-Best-Match

PingjunChen / GradingKneeOA

bio-ontology-research-group / opa2vec

epigen / enrichment_analysis

jvwilliams23 / pyssam

hisunjiang / Public-datasets-of-BCI

epigen / dea_limma

nikolamilosevic86 / verifAI

AnthonyMRios / adversarial-relation-classification

epigen / genome_tracks

dgidb / dgidb-v5

epigen / dea_seurat

hms-dbmi / EHRtemporalVariability

epigen / scrnaseq_processing_seurat

epigen / mixscape_seurat

epigen / spilterlize_integrate

gaoyuanliang / deep_depression_detector

mida-project / meta

jakelever / knowledgediscovery

bccummings / acq-tools

ushukkla / Test-The-Tongue

FAIRplus / Data-Maturity

i6092467 / pediatric-appendicitis-ml

YuxingLu613 / awesome-biomedical-knowledge-graphs

victorvicpal / biofes

SisonkeBiotik-Africa / MeSH2Matrix

StatBiomed / BMDS-book

carsaesi / covid19sdtool

fredhutchio / coding_for_cancer

Taneja24 / Semantic-Segmentation-of-Microscopy-Cell-Images