Software

Code repository for "Axon initial segment dynamics during associative fear learning"..

Spintge, Mai, Carraro et al., 2026: Single-cell multi-omic profiling allows the dissection of peripheral immune phenotypes in Alzheimer’s Disease progression The role of the peripheral immune system in Alzheimer’s Disease (AD) remains insufficiently resolved, limiting the understanding of systemic disease effects and mechanisms. Here, we employed three high-resolution single-cell techniques, including flow cytometry, single-cell RNA- and ATAC-sequencing, to investigate peripheral immunity in AD dementia and earlier stages of the AD trajectory in over 100 patients. [...]

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. The tools in this software implement various reconstruction algorithms for Magnetic Resonance Imaging. [...]

PyMyelinPSO version 1.0 is a Python framework for Particle Swarm Optimization (PSO)–based inversion of in-vivo and atlas MRI data (published by Dvorak et al., (2021). An atlas for human brain myelin content throughout the adult life span. [...]

Toolbox of Snakemake pipelines for easy-to-use analyses and benchmarks for building integrated atlases. This toolbox provides multiple modules that can be easily combined into custom workflows that leverage the file management of Snakemake. [...]

This is the analysis code used in our project on mean longitudinal resting-state and task functional connectivity within and between medial temporal lobe and posteromedial cortex in the PREVENT-AD cohort..

This repository contains the R script used for the analysis of single-cell RNA-sequencing (scRNA-seq) data to compare two experimental conditions: a control (CTRL) and CDDO-Me treatment (C3).The analysis pipeline performs the following steps:* **Data Loading and Pre-processing:** Loads 10x Genomics filtered feature-barcode matrices.* **Doublet Detection and Removal:** Identifies and filters out potential doublets using the `DoubletFinder` package.* **Quality Control (QC):** Filters cells based on nUMI, nGene, log10GenesPerUMI, and mitochondrial DNA ratio.* **Data Integration:** Merges the two conditions and corrects for batch effects using `Harmony`. Cell cycle effects and mitochondrial ratio are regressed out during scaling with `SCTransform`.* **Clustering and Visualization:** Performs dimensionality reduction (PCA and UMAP) and identifies cell clusters.* **Cell Type Annotation:** Includes code for renaming clusters based on marker gene expression.* **Differential Expression (DE) Analysis:** Identifies DE genes between conditions within specific cell clusters using `MAST`.* **Cell Signature Scoring:** Calculates gene signature scores using `UCell`.* **Cell-Cell Communication Analysis:** Infers and compares intercellular communication networks between the two conditions using `CellChat`..

cyCONDOR 0.3.1 changelog Added function condor_info to easily explore the content of a condor object. Solved Issue #31, color pallette is reversed in plot_marker_ridgeplot() function. [...]

This is the analysis code used in our project on precuneus activation during memory retrieval and its relation to amyloid burden in the PREVENT-AD cohort..

This is the analysis code used in our project on longitudinal resting-state functional connectivity in episodic memory brain areas in the PREVENT-AD cohort. We investigated changes over time in "normal aging" and with early Alzheimer's pathology as well as associations with cognitive performance..