Charlotte Soneson

22 papers Journal 21
YearRankTypeTitle / Venue / Authors
2025 J jnl
Building a continuous benchmarking ecosystem in bioinformatics.
PLoS Comput. Biol.
Izaskun Mallona, Charlotte Soneson, Ben Carrillo, Almut Lütge, Daniel Incicau, Reto Gerber, Anthony Sonrel, Mark D. Robinson
2025 J jnl
Eleven quick tips for writing a Bioconductor package.
PLoS Comput. Biol.
Charlotte Soneson, Lori A. Shepherd, Marcel Ramos, Kevin C. Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J. Carey
2025 J jnl
Learning and teaching biological data science in the Bioconductor community.
PLoS Comput. Biol.
Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedín C. Culhane, Sean R. Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan P. Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin C. Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson
2025 J jnl
ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets.
J. Open Source Softw.
Silvia Barbiero, Charlotte Soneson, Prisca Liberali, Michael B. Stadler
2024 J jnl
Learning and teaching biological data science in the Bioconductor community.
CoRR
Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedín C. Culhane, Sean Davis, Maria A. Doyle, Susan P. Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin C. Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson
2023 J jnl
einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data.
J. Open Source Softw.
Charlotte Soneson, Vytautas Iesmantavicius, Daniel Hess, Michael B. Stadler, Jan Seebacher
2022 J jnl
monaLisa: an R/Bioconductor package for identifying regulatory motifs.
Bioinform.
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schübeler, Michael B. Stadler
2021 J jnl
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.
PLoS Comput. Biol.
Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B. Stadler
2020 J jnl
TreeSummarizedExperiment: a S4 class for data with hierarchical structure.
F1000Research
Ruizhu Huang, Charlotte Soneson, Felix G. M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson
2020 J jnl
Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
PLoS Comput. Biol.
Michael I. Love, Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, N. Tessa Pierce, Lori A. Shepherd, Martin Morgan, Rob Patro
2019 J jnl
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats.
F1000Research
Lukas M. Weber, Charlotte Soneson
2018 J jnl
A systematic performance evaluation of clustering methods for single-cell RNA-seq data.
F1000Research
Angelo Duò, Mark D. Robinson, Charlotte Soneson
2018 J jnl
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.
F1000Research
Michael I. Love, Charlotte Soneson, Rob Patro
2018 J jnl
Towards unified quality verification of synthetic count data with countsimQC.
Bioinform.
Charlotte Soneson, Mark D. Robinson
2018 J jnl
iSEE: Interactive SummarizedExperiment Explorer.
F1000Research
Kevin C. Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T. L. Lun
2015 J jnl
Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness.
IEEE Trans. Pattern Anal. Mach. Intell.
Kerstin Johnsson, Charlotte Soneson, Magnus Fontes
2014 J jnl
Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings.
Comput. Stat. Data Anal.
Charlotte Soneson, Magnus Fontes
2014 J jnl
compcodeR - an R package for benchmarking differential expression methods for RNA-seq data.
Bioinform.
Charlotte Soneson
2013 J jnl
A comparison of methods for differential expression analysis of RNA-seq data.
BMC Bioinform.
Charlotte Soneson, Mauro Delorenzi
2011 — —
Statistically Guided Visualization and Exploratory Analysis of Omics Data.
Charlotte Soneson
2011 J jnl
The projection score - an evaluation criterion for variable subset selection in PCA visualization.
BMC Bioinform.
Magnus Fontes, Charlotte Soneson
2010 J jnl
Integrative analysis of gene expression and copy number alterations using canonical correlation analysis.
BMC Bioinform.
Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, Magnus Fontes