Preparing scRNA-seq and scATAC-seq data in h5ad format for use as input in MultiVI to infer latent representations.

GRN inference by pyscenic for scRNAseq data

visualizes mRNA-seq data interactively.

A Tensorflow-based multimodal baseline VAE model with a supervised classifier component to test on some small synthetic data incl. scRNAseq (trx read-by-cell), scATACseq (peak-by-cell) and Imaging …

Bayesian PRS methods model uncertainty in effect size estimates and shrink small effect sizes to mitigate spurious associations and biases from sample overlap. By using full posterior distributions…

Multiomics Pipeline by Mo De for FOUNDIN-1c: RNA Analysis Only

Automated pipeline for psuedobulk analysis and downstream unsupervised analysis based on seurat v5

Non negative matrix factorization for Oligo lineage scRNAseq data

This script utilizes Monocle3 for inferring pseudotime and employs gradient boosting machine learning (xgboost) to identify genes predictive of pseudotime. Subsequently, it fits a regression model …

single cell informed polygenic risk scoring in Parkinson's disease

This short script facilitates the conversion of binary genotypes to VCF format, followed by chromosome-specific splitting for subsequent imputation using Minimac4. It then performs a hard-call to s…

Leveraging the power of LD variational autoencoders to identify latent representations as dim red embeddings of sc data

Rscripts for PRS construction