Code for the analysis of 'Decoding injury responsive enhancers in the CNS for cell state targeting'

coTF-reg: Single-cell multi-omics analysis reveals cooperative transcription factors for gene regulation in oligodendrocytes

Scripts and datasets for the analysis on convergent genome evolution of animal terrestrialisation

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

R package for pathway analysis in scRNA-seq data

Nextflow training material

A simple visualisation tool for genomic tracks from sequencing experiments.

A pipeline for Nanopore single cell isoform quantification in R

A library of free open source icons for science illustrations in biology and chemistry

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

ATAC-seq and DNase-seq processing pipeline

Pipeline to identify isoforms from full-length cDNA sequencing data

LD Score Regression (LDSC)

Demultiplexing pooled scRNA-seq data with or without genotype reference

SUPPA: Fast quantification of splicing and differential splicing

Cell type prioritization in single-cell data

CUT&RUN and CUT&Tag data processing and analysis

Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).

Genome Structure Correction

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