Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

Wrapper of batch removal method for scRNA-seq

Basic scripts/markdowns for clustering and trajectory analysis

Reconstruction of complex single-cell trajectories using CellRouter

A Shiny app for visualizing and exploring single cell RNA-sequencing data

Single Cell RNA-seq UMI Filtering Facilitator

Plot_ly-based plotting functions for use with Seurat objects

Doublet detection in single-cell RNA-seq data (R package).

Collection of scripts used during internship at UMC Utrecht

Code for the analysis chapter of my PhD thesis looking at kidney organoid scRNA-seq data

Source Code for Single-Cell RNA-Seq Data Analysis

Create violin plots of gene expression for multiple genes

IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis

Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data

Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.

Ligand-Receptor Interaction map based on scRNA-seq and pathway enrichment

R package: {rfca} Random forest-based cell annotation methods for scRNAseq analysis. {rfca} contains methods which identifies cell types using machine learning trained on a diversity of cell types, without the need for a labelled training dataset. It also allows you to train your own cell prediction models with your own labels (cell type, subtyp…

I've written a few functions that help me look through scRNA-seq data while working with Seurat.

A statistical simulator for rational scRNA-seq experimental design