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Jesper Madsen's Projects

alevin-fry icon alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

conos icon conos

Clustering on Network of Samples

evolution icon evolution

This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'

glmmseq icon glmmseq

Gene-level general linear mixed model

harmony icon harmony

Scalable integration of single cell RNAseq data for batch correction and meta analysis

macs icon macs

MACS -- Model-based Analysis of ChIP-Seq

snrnaseq_ewat icon snrnaseq_ewat

Scripts for analysis of primary and supplementary snRNA-seq datasets from epididymal white adipose tissue from lean and obese mice.

tradeseq icon tradeseq

TRAjectory-based Differential Expression analysis for SEQuencing data

zumis icon zumis

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

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