Probabilistic Models in Biology

Probabilistic Models in Biology's repositories

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.

Language:HTMLApache-2.0108 18 27

deeprvat

Language:PythonNOASSERTION40 12 52

bicycle

Bicycle: Intervention-Based Causal Discovery with Cycles

Language:Jupyter Notebook36 10 1

MuDataSeurat

.h5mu files interface for Seurat

Language:R32 10 20

pycoMeth

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

Language:PythonGPL-3.030 2 9

SpatialDE

Test genes for Spatial Variation

Language:PythonMIT15 20

spatialdata-workshops

Language:Jupyter NotebookBSD-3-Clause13 9 5

mb-nanopore-2022

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

Language:PythonGPL-3.07 13 1

MetH5Format

HDF5-based container format for Methylation calls from long reads

Language:PythonMIT7 2 4

spaceTree

Language:Jupyter NotebookMIT7 9 1

Health-Privacy-Challenge

The starter kit for the CAMDA 2025 Health Privacy Challenge.

Language:PythonGPL-3.0600

MultiOmicsCourse

Language:Jupyter NotebookMIT5 130

scdali

scDALI: Modelling allelic imbalance in single cells.

Language:PythonBSD-3-Clause5 11 1

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".

Language:Jupyter Notebook4 100