Probabilistic Models in Biology

Pinned Repositories

bicycle
Bicycle: Intervention-Based Causal Discovery with Cycles
Language:Jupyter Notebook36 10 15
deepcpg
Deep neural networks for predicting CpG methylation
Language:Python37 7 013
deeprvat
Language:Python40 12 528
limix
We have moved to https://github.com/limix/limix.
Language:C++23 7 039
limix-backup
Language:C++45 10 1811
MuDataSeurat
.h5mu files interface for Seurat
Language:R32 10 2014
peer
A factor analysis package
Language:C++102 10 040
pycoMeth
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Language:Python30 2 93
pygp
A Gaussian process toolbox in python
Language:Python42 5 09
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:HTML108 18 2746

Probabilistic Models in Biology's Repositories

PMBio/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:HTML108 18 2746
PMBio/deeprvat
Language:Python40 12 528
PMBio/bicycle
Bicycle: Intervention-Based Causal Discovery with Cycles
Language:Jupyter Notebook36 10 15
PMBio/MuDataSeurat
.h5mu files interface for Seurat
Language:R32 10 2014
PMBio/pycoMeth
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Language:Python30 2 93
PMBio/SpatialDE
Test genes for Spatial Variation
Language:Python15 2 02
PMBio/spatialdata-workshops
Language:Jupyter Notebook13 9 56
PMBio/mb-nanopore-2022
Analysis code for publication "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signature"
Language:Python7 13 1
PMBio/MetH5Format
HDF5-based container format for Methylation calls from long reads
Language:Python7 2 41
PMBio/spaceTree
Language:Jupyter Notebook7 9 11
PMBio/Health-Privacy-Challenge
The starter kit for the CAMDA 2025 Health Privacy Challenge.
Language:Python68
PMBio/MultiOmicsCourse
Language:Jupyter Notebook5 13 0
PMBio/scdali
scDALI: Modelling allelic imbalance in single cells.
Language:Python5 11 11
PMBio/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 10 02
PMBio/mudatasets
Multimodal datasets, in MuData format
Language:Python4 3 61
PMBio/SingleCellCourse
Language:Jupyter Notebook4 16 09
PMBio/deeprvat-analysis
Language:Python3 9 10
PMBio/GBM_analysis
Notebooks and scripts used to analyse GBM multi-ome atlas
Language:Jupyter Notebook32
PMBio/scDoRI
Language:Python2
PMBio/ase_spermatogenesis
Language:HTML1 2 01
PMBio/hipsci_pipeline
Language:Python1 10 521
PMBio/muon.r
R ⇄ .h5mu I/O for multimodal data
Language:R1 5 3
PMBio/spatialde2-paper
Code to reproduce the figures (data not included)
Language:Jupyter Notebook1 3 2
PMBio/interp-extrap-perturb
https://interp-extrap-perturb.readthedocs.io
Language:Python00
PMBio/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
Language:Python1 0
PMBio/polygenic_germline_risk
Language:Jupyter Notebook
PMBio/remora
Methylation/modified base calling separated from basecalling.
Language:Python1 0
PMBio/scdali_analyses
Language:Jupyter Notebook8 0
PMBio/spatial-club-heidelberg
For scripts for downloading and processing data from different spatial technologies
10 0
PMBio/spava
Language:Python10 0