Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. - Charlotte Soneson; Henrik Lilljebjörn; Thoas Fioretos; Magnus Fontes (BMC Bioinform., 2010)

The projection score - an evaluation criterion for variable subset selection in PCA visualization. - Magnus Fontes; Charlotte Soneson (BMC Bioinform., 2011)

Statistically Guided Visualization and Exploratory Analysis of Omics Data. - Charlotte Soneson (2011)

A comparison of methods for differential expression analysis of RNA-seq data. - Charlotte Soneson; Mauro Delorenzi (BMC Bioinform., 2013)

compcodeR - an R package for benchmarking differential expression methods for RNA-seq data. - Charlotte Soneson (Bioinform., 2014)

Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings. - Charlotte Soneson; Magnus Fontes (Comput. Stat. Data Anal., 2014)

Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness. - Kerstin Johnsson; Charlotte Soneson; Magnus Fontes (IEEE Trans. Pattern Anal. Mach. Intell., 2015)

Towards unified quality verification of synthetic count data with countsimQC. - Charlotte Soneson; Mark D. Robinson (Bioinform., 2018)

A systematic performance evaluation of clustering methods for single-cell RNA-seq data. - Angelo Duò; Mark D. Robinson; Charlotte Soneson (F1000Research, 2018)

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification. - Michael I. Love; Charlotte Soneson; Rob Patro (F1000Research, 2018)

iSEE: Interactive SummarizedExperiment Explorer. - Kevin C. Rue-Albrecht; Federico Marini 002; Charlotte Soneson; Aaron T. L. Lun (F1000Research, 2018)

HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. - Lukas M. Weber; Charlotte Soneson (F1000Research, 2019)

TreeSummarizedExperiment: a S4 class for data with hierarchical structure. - Ruizhu Huang; Charlotte Soneson; Felix G. M. Ernst; Kevin C. Rue-Albrecht; Guangchuang Yu; Stephanie C. Hicks; Mark D. Robinson (F1000Research, 2020)

Tximeta: Reference sequence checksums for provenance identification in RNA-seq. - Michael I. Love; Charlotte Soneson; Peter F. Hickey; Lisa K. Johnson; N. Tessa Pierce; Lori A. Shepherd; Martin Morgan; Rob Patro (PLoS Comput. Biol., 2020)

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. - Charlotte Soneson; Avi Srivastava; Rob Patro; Michael B. Stadler (PLoS Comput. Biol., 2021)

monaLisa: an R/Bioconductor package for identifying regulatory motifs. - Dania Machlab; Lukas Burger; Charlotte Soneson; Filippo M. Rijli; Dirk Schübeler; Michael B. Stadler (Bioinform., 2022)

einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data. - Charlotte Soneson; Vytautas Iesmantavicius; Daniel Hess; Michael B. Stadler; Jan Seebacher (J. Open Source Softw., 2023)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean Davis 001; Maria A. Doyle; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; Kozo Nishida; Marcel Ramos; et al. (CoRR, 2024)

The Journal of Open Source Software (JOSS) - Bringing open-source software practices to the scholarly publishing community for authors, reviewers, editors, and publishers. - Patrick Diehl; Charlotte Soneson; Rachel C. Kurchin; Ross Mounce; Daniel S. Katz (Zenodo, 2024)

The Journal of Open Source Software (JOSS) - Bringing open-source software practices to the scholarly publishing community for authors, reviewers, editors, and publishers. - Patrick Diehl; Charlotte Soneson; Rachel C. Kurchin; Ross Mounce; Daniel S. Katz (Zenodo, 2024)

Learning and teaching biological data science in the Bioconductor community. - 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; et al. (PLoS Comput. Biol., 2025)

Eleven quick tips for writing a Bioconductor package. - Charlotte Soneson; Lori A. Shepherd; Marcel Ramos; Kevin C. Rue-Albrecht; Johannes Rainer; Hervé Pagès; Vincent J. Carey (PLoS Comput. Biol., 2025)

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. - Silvia Barbiero; Charlotte Soneson; Prisca Liberali; Michael B. Stadler (J. Open Source Softw., 2025)