Alma Andersson

her2st. Her2 Breast Cancer Project

stereoscope. Spatial mapping of cell types by integration of transcriptomics data

eggplant. Jupyter Notebook

ST-mLiver. Code associated with the manuscript Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver

diceconverter. Python

growmeatissue. Synthethic data generation

genetech. material related to the genetech courses

sepal. sepal : Spatial Expression PAttern Locator

CellTracker. Implementation of the Gaussian Mixture Particle Hypothesis Density (GM-PHD) filter for cell tracking in brightfield images

flash-scope. A speedy implementation of stereoscope

Cluster-VAE. Clustering of Single Cell or ST-data using a Variational Autoencoder for dimensionality reduction followed by a Dirichlet Process based unsupervised clustering

space2h5ad. Automatic conversion of spacerange output to h5ad format

star-repair. Python

scCBGM. Jupyter Notebook

ST_subtype_classification. subtype classification of breast cancer based on ST-data, using markov random fields and neural networks.

axis-projection. R

spacetx. scripts related to work with spacetx

breast_dge. Breast Cancer Differential Gene Expression Analysis Project