petVAE
Amyloid PET subgroups
2D convolutional variational autoencoders for modeling the Alzheimer's disease continuum and identifying amyloid PET subgroups.
Python · 1 stars · updated Jan 2026
Software
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ionstats
DNA adducts from nanopore signal
Compound-specific DNA adduct profiling straight from nanopore ionic current.
Python · 3 stars · updated Oct 2025
PaVaDi
Pathogenicity evaluation of germline variants
Pipeline for evaluating coding germline variants at cohort scale, used to find rare alleles enriched in hematological patients of the Finnish founder population.
Python · 1 stars · updated Oct 2025
HistoEncoder
Foundation model for prostate histology
A digital pathology foundation model trained on prostate cancer tissue, with encoders you can drop into your own downstream task instead of training from scratch.
Python · 43 stars · updated Sep 2025
arched
CSF amyloid-beta from PET images
ArcheD, a residual network that predicts cerebrospinal fluid amyloid-beta directly from amyloid PET images, independent of brain region.
Jupyter Notebook · 1 stars · updated Sep 2025
blood-cell-painting-paper
Blood Cell Painting analysis
Full analysis code for morphological single-cell profiling of peripheral blood mononuclear cells from 390 healthy blood donors.
Jupyter Notebook · 2 stars · updated Sep 2025
ERCC6L2-scRNA
Single-cell analysis for the ERCC6L2 and Shwachman-Diamond study
Analysis code for the HemaSphere paper: single-cell RNA sequencing of bone marrow in ERCC6L2 disease and Shwachman-Diamond syndrome, from preprocessing to the stem cell identities and the shared erythroid stress signature.
Python · 2 stars · updated Sep 2025
muat
Tumor classification from somatic variants
Portable transformer that reads a patient's somatic variants and returns tumor type, subtype and a learned representation. Available as a conda package.
Python · 8 stars · updated Aug 2025
mutation-attention
MuAt, the model behind the method
Reference implementation of Mutation-Attention: deep representation learning of somatic mutations for tumour typing and subtyping, as published in Genome Medicine.
Python · 6 stars · updated Apr 2025
StrongAugment
Augmentation against domain shift in digital pathology
Strong augmentation for training histopathology models that hold up on slides from other scanners, stains and laboratories, as measured in the fragility study.
Python · 9 stars · updated Sep 2023
DeepIFC
Virtual fluorescent labels for blood cells
Generates fluorescent-channel images from brightfield imaging flow cytometry, allowing blood cell phenotypes to be read without staining every channel.
Python · 1 stars · updated Mar 2023
BasePlayer
Variant discovery across large sequencing cohorts
Interactive browser for finding causative variants in coding and noncoding genome, combining data integration, comparison and visualization in one view. BasePlayer 2, an enhanced version of BasePlayer, is currently in development and will natively support multimodal data, including long-read and methylation sequencing.
Java · 5 stars · updated Mar 2020