User profiles for R. Cannoodt

Robrecht Cannoodt

Computer Science Engineer at Data Intuitive
Verified email at ugent.be
Cited by 3779

Computational methods for trajectory inference from single‐cell transcriptomics

R Cannoodt, W Saelens, Y Saeys - European journal of …, 2016 - Wiley Online Library
Recent developments in single‐cell transcriptomics have opened new opportunities for studying
dynamic processes in immunology in a high throughput and unbiased manner. Starting …

[HTML][HTML] Essential guidelines for computational method benchmarking

LM Weber, W Saelens, R Cannoodt, C Soneson… - Genome biology, 2019 - Springer
… This website was created using the Shiny framework in R … , the command ‘sessionInfo()’
gives a complete summary of package versions, the version of R, and the operating system. For …

A scalable SCENIC workflow for single-cell gene regulatory network analysis

…, S Aibar, R Seurinck, W Saelens, R Cannoodt… - Nature protocols, 2020 - nature.com
… and enables integration with the R version of the method. Instructions for integration with …
For the initial R-based version, we refer the reader to the vignettes available online (https://…

A comparison of single-cell trajectory inference methods

W Saelens, R Cannoodt, H Todorov, Y Saeys - Nature biotechnology, 2019 - nature.com
… Each task was allocated one CPU core of an Intel(R) Xeon(R) CPU E5-2665 at 2.40 GHz,
and one R session was started for each task. During the execution of a method on a dataset, if …

[HTML][HTML] Trajectory-based differential expression analysis for single-cell sequencing data

…, K Street, W Saelens, R Cannoodt… - Nature …, 2020 - nature.com
Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the
study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital to …

[HTML][HTML] Recent advances in trajectory inference from single-cell omics data

L Deconinck, R Cannoodt, W Saelens… - Current Opinion in …, 2021 - Elsevier
… A unifying framework to characterize TI methods has been proposed by Cannoodt et al. [1].
In a first step, most methods apply some sort of dimensionality reduction method to reduce …

[HTML][HTML] A comprehensive evaluation of module detection methods for gene expression data

W Saelens, R Cannoodt, Y Saeys - Nature communications, 2018 - nature.com
A critical step in the analysis of large genome-wide gene expression datasets is the use of
module detection methods to group genes into co-expression modules. Because of limitations …

The RNA Atlas expands the catalog of human non-coding RNAs

…, F Avila Cobos, S Gross, PJ Volders, R Cannoodt… - Nature …, 2021 - nature.com
Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are
derived almost exclusively from small and polyadenylated RNAs. Here we present a more …

[PDF][PDF] The transcription factor ZEB2 is required to maintain the tissue-specific identities of macrophages

…, J Bonnardel, S De Prijck, N Vandamme, R Cannoodt… - Immunity, 2018 - cell.com
Heterogeneity between different macrophage populations has become a defining feature of
this lineage. However, the conserved factors defining macrophages remain largely unknown…

[HTML][HTML] Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

R Cannoodt, W Saelens, L Deconinck… - Nature …, 2021 - nature.com
… Since no implementation was provided by the authors, we implemented SSN in R using basic
R and … Results in this manuscript were generated with R 4.0.3 and dyngen 1.0.0. dyngen is …