article-journal

Eleven quick tips for writing a Bioconductor package

Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J Carey

Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth

Samuel D Gamboa-Tuz, Marcel Ramos, Eric Franzosa, Curtis Huttenhower, Nicola Segata, Sehyun Oh, Levi Waldron

lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R

Asya Khleborodova, Samuel D Gamboa-Tuz, Marcel Ramos, Nicola Segata, Levi Waldron, Sehyun Oh

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines

Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Michael C Schatz, Sean Davis, Vincent Carey, Martin Morgan, Levi Waldron

Learning and teaching biological data science in the Bioconductor community

Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Sean Davis, Maria A Doyle, Ludwig Geistlinger, Andrew R Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J H Shih, Laurent Gatto, Charlotte Soneson

Curated single cell multimodal landmark datasets for R/Bioconductor

Kelly B Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin C Culhane, Laurent Gatto, Vincent Carey, Martin Morgan, Davide Risso, Levi Waldron

RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor

Marcel Ramos, Martin Morgan, Ludwig Geistlinger, Vincent J Carey, Levi Waldron

GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N Taroni, Vincent J Carey, Casey S Greene, Levi Waldron, Sean Davis

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Michael C Schatz, Anthony A Philippakis, Enis Afgan, Eric Banks, Vincent J Carey, Robert J Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L Grossman, Ira M Hall, Kasper D Hansen, Jonathan Lawson, Jeffrey T Leek, Anne O'donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D O'Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet

Toward a gold standard for benchmarking gene set enrichment analysis

Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron