Explore @MarioniLab Open Source projects

Marioni Laboratory (@MarioniLab)

MarioniLab

Stars
838
Global Org. Rank 17,316 (Top 6 %)
Registered almost 9 years ago
Most used languages

R
53.2 %

HTML
21.0 %

Jupyter Notebook
8.1 %

TeX
6.5 %

Shell
4.8 %

Python
3.2 %

Makefile 1.6 %

PostScript 1.6 %
Location 🇬🇧 United Kingdom
Country Total Rank 1,753
Country Ranking

R
11

PostScript 21

TeX
102

HTML
193

Makefile 327

Jupyter Notebook
576

Shell
1,541

Python
5,972

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

EmbryoTimecourse2018

Data and analysis scripts for our Embryo Timecourse paper.

miloDE

Framework for sensitive DE testing (using neighbourhoods)

DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

MNN2017

Code for the MNN manuscript figures

scran

Clone of the Bioconductor repository for the scran package.

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

Jupyter Notebook

EmptyDrops2017

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

Deconvolution2016

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

SpatialMouseAtlas2020

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

oor_design_reproducibility

Jupyter Notebook

sarlacc

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.

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

milo_analysis_2020

Code to reproduce analysis of Milo manuscript

MouseGastrulationData

Clone of the Bioconductor repository for the MouseGastrulationData package.

ImmuneAging2017

Code for Celia and Nils' immune aging project.

BarcodeSwapping2017

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

EmptyDropsMultiome

Removing empty droplets in multiome datasets

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)

Spermatogenesis2018

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

PlateEffects2016

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

Aneuploidy2017

Supplementary files for our Aneuploidy Detection paper

MammaryGland

StabMap2021

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

CELLOseq

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

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

Jupyter Notebook

ZikaPsolaren2017

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

mouseHeart_2020

SpikeIns2016

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

simpleSingleCellResults

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

EmptyDropsMultiome2023_final

XenopusTailRegeneration2019

am_geneBasis

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

Jupyter Notebook

gastruloids2022

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

Jupyter Notebook

SingleCellRetina2016

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

TChimeras2020

amScripts_mouseEmbryoFISH

scripts regarding FISH data of gastrulating mouse embryo (amissarova)

FurtherNorm2018

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

miloDE_analysis

Folder contains scripts to generate and analyse data for miloDE

OesophagusSingleCell2018

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

milo

Differential abundance on KNN graphs

XenopusLimbRegeneration2020

Adipogenesis2018

R markdown notebooks and scripts for the Adipogenesis manuscript

EmbryoData2018

scRNAseqLungNKcells

LncScreen2018

Code for Lovorka and Aaron's lncRNA screen paper.

ExtendedMouseAtlas

cydar

Clone of the Bioconductor repository for the cydar package.

scSNV-seq

long_read_simulations

Long-read sequencing simulation evaluations