Software

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..

cyCONDOR 0.3.0 changelog Bug fix with data projection where specific parameters were removed in UMAP calculation Updated official Docker image to the latest Bioconductor version (Bioconductor 3.20, R 4.4.2) Completed documentation of the Astir workflow. Added parameter to select number of PCs and markers for UMAP projection in learnUMAP function. [...]

Population-scale multi-layered datasets assemble extensive experimental data of different types on single healthy individuals in large cohorts, capturing genetic variation and environmental factors influencing gene expression with no clinical evidence of pathology. Variance of gene expression can be exploited to set up a conditional quasi loss- and gain-of-function “in population” experiment if expression values for the gene of interest (GOI) are available [...]

Population-scale multi-layered datasets assemble extensive experimental data of different types on single healthy individuals in large cohorts, capturing genetic variation and environmental factors influencing gene expression with no clinical evidence of pathology. Variance of gene expression can be exploited to set up a conditional quasi loss- and gain-of-function “in population” experiment if expression values for the gene of interest (GOI) are available [...]

jemris (2.9-0) stable; urgency=low Major added image reconstruction and ismrmrd support Major added deformable motion simulation Major simulation performance improvement Major revived multi-pool MRI simulations based on the Bloch-McConnel equations Minor bug fixes Minor updated documentation

First stable release of AAanalysis (Amino Acid analysis), a Python framework for interpretable sequence-based protein prediction. This version includes the foundational algorithms used in the publication 'Charting γ-secretase substrates by explainable AI' (Breimann & Kamp et al., Nature Communications, 2025): CPP (Comparative Physicochemical Profiling), a feature engineering method that identifies the most distinctive physicochemical properties between two sets of protein sequences, and dPULearn, a deterministic positive-unlabeled (PU) learning algorithm enabling robust classification from imbalanced and small datasets..

This repository contains code to model functional activity of opsins based on the spectral density template developed by Govardovskii et al. (2000). [...]