Discover MarioniLab/EmptyDropsMultiome2023

Framework for sensitive DE testing (using neighbourhoods)

miloDE

DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

MNN2017

Code for the MNN manuscript figures

Clone of the Bioconductor repository for the scran package.

scran

StabMap

Mosaic single cell data integration using non-overlapping features

FurtherMNN2018

Code for further development of the mutual nearest neighbours batch correction method, as implemented in the batchelor package.

hbca

Code used to process the data of the HBCA project

sagenet

Spatial reconstruction of dissociated single-cell data

Code for the empty droplet and cell detection project from the HCA Hackathon.

EmptyDrops2017

Code and manuscript files for Aaron and Karsten's deconvolution paper.

Deconvolution2016

Data processing and analysis scripts for our spatial profiling of embryos using seqFISH

SpatialMouseAtlas2020

oor_design_reproducibility

The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, clusters reads and produces a consensus sequence for each cluster after multiple sequence alignment.

sarlacc

geneBasisR

R package for gene selection using k-NN graphs.

oor_benchmark

A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data

Python

milo_analysis_2020

Code to reproduce analysis of Milo manuscript

Clone of the Bioconductor repository for the MouseGastrulationData package.

MouseGastrulationData

ImmuneAging2017

Code for Celia and Nils' immune aging project.

BarcodeSwapping2017

Supplementary files for paper "Detection and removal of barcode swapping in single-cell RNAseq".

Removing empty droplets in multiome datasets

EmptyDropsMultiome

compareSingleCell

Workflows for comparative analyses of single-cell RNA sequencing data, migrated to the OSCA book.

scHOT2019

Instructions and analysis scripts for single cell Higher Order Testing (scHOT)

Code for Christina and Nils' project to dissect spermatogenesis in mice

Spermatogenesis2018

PlateEffects2016

Code and manuscript files for Aaron's plate effect paper.

PostScript

Aneuploidy2017

Supplementary files for our Aneuploidy Detection paper

Analysis scripts for 'StabMap: Mosaic single cell data integration using non-overlapping features'

MammaryGland

StabMap2021

CELLOseq

Transposable element expression at unique loci in single cells with CELLO-seq

Shell

archive-scran

An archived version of the scran repository, see https://github.com/MarioniLab/scran for the active version.

archive-cydar

An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.

simpleSingleCell

Clone of the Bioconductor repository for the simpleSingleCell workflow.

RegressionBASiCS2017

Analysis code for Nils and Catalina's regression extension

NaiveHESC2016

Code for Tobias, Ferdinand and Aaron's naive/primed hESC project.

CovidPBMC

Single-cell analysis of Covid-19 patient PBMCs

Tumorigenesis2018

EmbryoTimecourseShiny

Shiny scripts for the embryo timecourse dataset

archive-simpleSingleCell

An archived version of the simpleSingleCell repository, see https://github.com/MarioniLab/simpleSingleCell for the active version.

RabbitGastrulation2022

Code for Omer's Zika virus Psolaren cross-linking project.

ZikaPsolaren2017

Shell

mouseHeart_2020

Code and manuscript files for Aaron's spike-in manuscript.

SpikeIns2016

Compiled reference results for the simpleSingleCell workflow at https://github.com/MarioniLab/simpleSingleCell.

simpleSingleCellResults

Makefile

XenopusTailRegeneration2019

prediction of marker genes for cell typing and spatial gradients from scRNA-seq

am_geneBasis

Code for the 2022 paper "Inter-gastruloid heterogeneity revealed by single cell transcriptomics time course: implications for organoid based perturbation studies"

gastruloids2022

Code for Mike and Aaron's analysis of single-cell cone photoreceptor transcriptomics data

SingleCellRetina2016

TChimeras2020

scripts regarding FISH data of gastrulating mouse embryo (amissarova)

amScripts_mouseEmbryoFISH

Code for further development of the summation-based scaling normalization method, as implemented in the scran package.

FurtherNorm2018

miloDE_analysis

Folder contains scripts to generate and analyse data for miloDE

Code for the single cell project on normal oesophagus and Barrett's oesophagus

OesophagusSingleCell2018

milo

Differential abundance on KNN graphs

R markdown notebooks and scripts for the Adipogenesis manuscript

XenopusLimbRegeneration2020

Adipogenesis2018

EmbryoData2018

Shell

scRNAseqLungNKcells

LncScreen2018

Code for Lovorka and Aaron's lncRNA screen paper.

ExtendedMouseAtlas

cydar

Clone of the Bioconductor repository for the cydar package.

scSNV-seq