Probabilistic Models in Biology

scLVM

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.

bicycle

Bicycle: Intervention-Based Causal Discovery with Cycles

pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

deeprvat

MuDataSeurat

.h5mu files interface for Seurat

scMT-seq

SpatialDE

Test genes for Spatial Variation

MetH5Format

HDF5-based container format for Methylation calls from long reads

mb-nanopore-2022

Analysis code for publication "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signature"

Rslalom

slalom - an R package implementing a factorial single cell latent variable model

scdali

scDALI: Modelling allelic imbalance in single cells.

SingleCellCourse

MB_scSeq

This repo contains scripts for the analysis of scDNA- and scSeq data from LFS medulloblastoma accompanying the manuscript "SINGLE CELL MULTI-OMICS ANALYSIS OF CHROMOTHRIPTIC MEDULLOBLASTOMA HIGHLIGHTS GENOMIC AND TRANSCRIPTOMIC CONSEQUENCES OF GENOME INSTABILITY".

MultiOmicsCourse

scmt_splicing

mudatasets

Multimodal datasets, in MuData format

deeprvat-analysis

hipsci_pipeline

muon.r

R ⇄ .h5mu I/O for multimodal data

stepwise-elnet

Code to perform step wise elastic net analysis

ase_spermatogenesis

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

hca_organoid_pipelines

Pipelines for HCA|Organoid data processing

remora

Methylation/modified base calling separated from basecalling.

scdali_analyses

spaceTree

spatial-club-heidelberg

For scripts for downloading and processing data from different spatial technologies

spatialdata-workshops

spatialde2-paper

Code to reproduce the figures (data not included)

spava