marionilab Goto Github PK

adipogenesis2018

R markdown notebooks and scripts for the Adipogenesis manuscript

am_genebasis

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

amscripts_mouseembryofish

scripts regarding FISH data of gastrulating mouse embryo (amissarova)

aneuploidy2017

Supplementary files for our Aneuploidy Detection paper

archive-cydar

An archived version of the cydar repository, see https://github.com/MarioniLab/cydar for the active version.

archive-scran

An archived version of the scran repository, see https://github.com/MarioniLab/scran for the active version.

archive-simplesinglecell

An archived version of the simpleSingleCell repository, see https://github.com/MarioniLab/simpleSingleCell for the active version.

barcodeswapping2017

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

be_perturb_seq_drug_resistance

celloseq

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

commonresources

Common lab resources for processing sequencing data

comparesinglecell

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

comparesinglecellresults

Compiled reference results for the compareSingleCell workflow.

covidpbmc

Single-cell analysis of Covid-19 patient PBMCs

cpgisland2017

Code for Mike's CpG island noise manuscript

ctlstimulation

Analysis of RNAseq and mass spectrometry data of stimulated cytotoxic T lymphocytes to understand the role of transcription

cydar

Clone of the Bioconductor repository for the cydar package.

damethods2016

Code and manuscript files for Aaron and Arianne's differential abundance methodology manuscript.

deconvolution2016

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

dropletutils

Clone of the Bioconductor repository for the DropletUtils package.

embryodata2018

embryotimecourse2018

Data and analysis scripts for our Embryo Timecourse paper.

embryotimecourseshiny

Shiny scripts for the embryo timecourse dataset

emptydrops2017

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

emptydropsmultiome

Removing empty droplets in multiome datasets

emptydropsmultiome2023_final

extendedmouseatlas

furthermnn2018

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

furthernorm2018

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

gammadeltatcells2018

Code for the gamma delta T cell project with Maike De La Roche, Hung-Chang Chen and Celia Martinez