A collection of UNet and hybrid architectures in PyTorch for 2D and 3D Biomedical Image segmentation
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Aug 2, 2018 - Python
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biomedical-data-science
Here are 131 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
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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
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Apr 22, 2023 - Jupyter Notebook
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
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Feb 23, 2023 - Python
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
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Mar 10, 2025 - 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
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Dec 2, 2022 - C++
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
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Feb 9, 2022 - Python
Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches
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Apr 30, 2018 - 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
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Jan 31, 2025 - Python
Turning Ontologies Plus Annotation Properties into Vectors
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Sep 26, 2020 - Groovy
A Python library for biomedical statistical shape and appearance modelling.
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Jun 19, 2024 - Python
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
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Mar 6, 2025 - R
Providing interactions between drugs and genes sourced from a variety of publications and knowledgebases
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Apr 24, 2025 - Ruby
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
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Dec 20, 2024 - 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
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Dec 20, 2024 - 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
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Dec 20, 2024 - 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
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Dec 20, 2024 - R
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
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Mar 4, 2025 - R
Unsupervised domain adaptation method for relation extraction
nlp machine-learning natural-language-processing bioinformatics nlp-machine-learning relation-extraction biomedical-data-science
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Jul 16, 2018 - Python
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