ConstantinAhlmann-Eltze

Postdoc

UCL London

Biography

I am a postdoc at Cancer Institute at UCL in the group of James Reading. I did my PhD with Wolfgang Huber at EMBL Heidelberg. Before joining UCL, I did a bridging postdoc with Simon Anders at Heidelberg University.

Currently, I am working on novel ways to analyze the role of T cells in early cancerogenesis.

Previously, I have worked on:

Statistical methods to simplify working with single-cell data,
Benchmarks of single-cell methods,
Differential abundance analysis of mass spectrometry data,
Clustering of high-dimensional categorical data.

For a full record of my publications, see Google scholar.

In addition, I develop statistical methods and tools for the analysis of cutting edge biological data. I maintain ten R packages which are published on CRAN and Bioconductor and total more than 100,000 downloads per month. In 2023, I received the Bioconductor community award in recognition of my contributions to the project.

If you are working in a company and would like help with some analysis or one of my packages, please get in touch, as I am happy to consult on projects.

Recent Posts

Latex to Word conversion with pandoc

Converting arbitrary Latex documents to Word documents without errors is probably impossible. However, pandoc can get you surprisingly …

Last updated on Aug 2, 2024 4 min read

tidyselect and tidyeval cheat sheet

How to refer to columns when programming with dplyr.

Oct 23, 2023 3 min read

My R package downloads

Download statistics of my R packages.

Sep 10, 2023 1 min read

ggplot2 minimum point size

Remove the stroke around points to map the size argument accurately.

Jun 9, 2023 2 min read

What is the delta method?

Find the standard deviation of $g(X)$

Feb 10, 2023 3 min read

Recent Publications

Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods

Comparison of foundation models for genetic perturbation prediction against linear models.

Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders (2023). bioR$\chi$iv

PDF DOI Reproducibility Github

Comparison of transformations for single-cell RNA-seq data

Theoretical and empirical analysis of transformation methods for single-cell data.

Constantin Ahlmann-Eltze, Wolfgang Huber (2023). Nat. Methods

PDF Project DOI Reproducibility R package Github Shiny App

Analysis of multi-condition single-cell data with latent embedding multivariate regression

A new method to analyze multi-condition single-cell data without clustering

Constantin Ahlmann-Eltze, Wolfgang Huber (2023). bioR$\chi$iv

PDF Project DOI Github

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data

Fit Gamma-Poisson Generalized Linear Models Reliably.

Constantin Ahlmann-Eltze, Wolfgang Huber (2020). Bioinformatics

PDF Project DOI Reproducibility R package Github

proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry

Decide which proteins are differentially abundant in label-free mass spectormetry without imputation.

Constantin Ahlmann-Eltze, Simon Anders (2019). bioR$\chi$iv

PDF Project DOI Reproducibility R package Github

See all publications

Software

ggupset

Bezier curves for ggplot2.

lemur

R package for “Latent Embedding Multivariate Regression”

pyLemur

Python package for “Latent Embedding Multivariate Regression”

transformGamPoi

Variance stabilizing transformation for Gamma Poisson distributed data

einsum

Einstein Summation for Arrays in R

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

sparseMatrixStats

Implementation of the matrixStats API for sparse matrices

proDA

R package for “Protein Differential Abundance Analysis for Label-Free Mass Spectrometry Data”

ggupset

Plot a combination matrix instead of the standard x-axis and create UpSet plots with ggplot2.

mixdir

R package for clustering high dimensional categorical data

tidygenomics

Tidy Verbs for Dealing with Genomic Data Frames

ggsignif

A ggplot2 extension to add significance brackets