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ase_spermatogenesis

bicycle

Bicycle: Intervention-Based Causal Discovery with Cycles

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

cyclone

cyclone

deepcpg

Deep neural networks for predicting CpG methylation

deeprvat

deeprvat-analysis

envgplvm

PANAMA and LIMMI models

gnetlmm

gptwosample

GPtwosample

gwatools

gwatools

hca_organoid_pipelines

Pipelines for HCA|Organoid data processing

hipsci_pipeline

limix

We have moved to https://github.com/limix/limix.

limix-backup

limix-feedstock

A conda-smithy repository for limix.

limix-tutorials

Limix tutorials and demos

mb-nanopore-2022

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

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".

meth5format

HDF5-based container format for Methylation calls from long reads

mtset

mtSet is an implementation of efficient set test algorithms for joint analysis across multiple traits. mtSet can account for confounding factors such as relatedness and can be used for analysis of single traits.

mudatasets

Multimodal datasets, in MuData format

mudataseurat

.h5mu files interface for Seurat

multiomicscourse

muon.r

R ⇄ .h5mu I/O for multimodal data

peer

A factor analysis package

pycometh

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

pygp

A Gaussian process toolbox in python

pygp_kronsum

remora

Methylation/modified base calling separated from basecalling.