A collection of UNet and hybrid architectures in PyTorch for 2D and 3D Biomedical Image segmentation
-
Updated
Aug 2, 2018 - Python
#
biomedical-data-science
Here are 139 public repositories matching this topic...
A Curated List of Computational Biology Datasets Suitable for Machine Learning
machine-learning computational-biology dataset curated-list datasets biomedical-data-science computational-biology-datasets
-
Updated
Apr 19, 2024
UNet based model that segment retina to 8 layers in OCT images
python machine-learning deep-neural-networks deep-learning images neural-networks segmentation image-segmentation biomedical-image-processing keras-tensorflow computer-vision-algorithms biomedical-data-science retinal-layer-segmentation
-
Updated
Apr 22, 2023 - Jupyter Notebook
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
-
Updated
Aug 5, 2025 - Python
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.
machine-learning computational-biology pytorch uncertainty mri unet microscopy uncertainty-quantification uncertainty-estimation biomedical-image-processing computational-imaging biomedical-data-science quantile-regression image-to-image-translation
-
Updated
Feb 23, 2023 - Python
A software package for statistically significant shapelet mining
time-series biomedical time-series-analysis shapelets biomedical-data-science time-series-analysis-tool significant-pattern-mining
-
Updated
Dec 2, 2022 - C++
Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches
-
Updated
Apr 30, 2018 - Python
Knee Osteoarthritis Analysis with X-ray Images using CNN
deep-learning biomedical-data-science yolov2 x-ray-images cnn-classification grading-system knee-joints knee-osteoarthritis-analysis kl-grading
-
Updated
Feb 9, 2022 - Python
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
visualization workflow bioinformatics gene-sets rna-seq snakemake pipeline chip-seq atac-seq gene-set-enrichment enrichment-analysis genomic-regions biomedical-data-science motif-enrichment-analysis
-
Updated
Aug 5, 2025 - Python
Turning Ontologies Plus Annotation Properties into Vectors
-
Updated
Sep 26, 2020 - Groovy
A Python library for biomedical statistical shape and appearance modelling.
-
Updated
Jun 19, 2024 - Python
Providing interactions between drugs and genes sourced from a variety of publications and knowledgebases
-
Updated
Jul 17, 2025 - Ruby
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
visualization workflow bioinformatics rna-seq snakemake r statistics scrna-seq chip-seq atac-seq limma biomedical-data-science differential-expression-analysis volcano-plot limma-voom limma-trend
-
Updated
Jul 21, 2025 - R
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.
visualization python workflow bioinformatics rna-seq snakemake pipeline scrna-seq atac-seq genome-browser genomic-regions biomedical-data-science genome-track
-
Updated
Aug 5, 2025 - Python
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.
visualization workflow bioinformatics snakemake scrna-seq single-cell 10xgenomics biomedical-data-science cite-seq snrna-seq sccrispr-seq
-
Updated
Jun 23, 2025 - R
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
visualization workflow bioinformatics snakemake scrna-seq single-cell biomedical-data-science differential-expression-analysis volcano-plot snrna-seq
-
Updated
Jun 23, 2025 - R
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.
visualization workflow bioinformatics snakemake scrna-seq single-cell biomedical-data-science perturbation-analysis snrna-seq sccrispr-seq
-
Updated
Jun 23, 2025 - R
SCassist : An AI Based Workflow Assistant for Single-Cell Analysis
bioinformatics computational-biology artificial-intelligence omics biomedical-data-science single-cell-rna-seq personalized-medicine single-cell-analysis gemini-api rnase llm ollama llama3
-
Updated
Jul 18, 2025 - HTML
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.
visualization workflow bioinformatics rna-seq snakemake integration pipeline ngs dimensionality-reduction chip-seq atac-seq normalization biomedical-data-science batch-effect count-matrix confounding-effects
-
Updated
Jul 9, 2025 - R
Improve this page
Add a description, image, and links to the biomedical-data-science topic page so that developers can more easily learn about it.
Add this topic to your repo
To associate your repository with the biomedical-data-science topic, visit your repo's landing page and select "manage topics."