article-journal

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

HGNChelper: identification and correction of invalid gene symbols for human and mouse

Sehyun Oh, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos, Sean Davis, Markus Riester, Levi Waldron

Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma

Ludwig Geistlinger, Sehyun Oh, Marcel Ramos, Lucas Schiffer, Rebecca S LaRue, Christine M Henzler, Sarah A Munro, Claire Daughters, Andrew C Nelson, Boris J Winterhoff, Zenas Chang, Shobhana Talukdar, Mihir Shetty, Sally A Mullany, Martin Morgan, Giovanni Parmigiani, Michael J Birrer, Li-Xuan Qin, Markus Riester, Timothy K Starr, Levi Waldron

Multiomic Integration of Public Oncology Databases in Bioconductor

Marcel Ramos, Ludwig Geistlinger, Sehyun Oh, Lucas Schiffer, Rimsha Azhar, Hanish Kodali, Ino de Bruijn, Jianjiong Gao, Vincent J Carey, Martin Morgan, Levi Waldron

Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale

Vincent J Carey, Marcel Ramos, Benjamin J Stubbs, Shweta Gopaulakrishnan, Sehyun Oh, Nitesh Turaga, Levi Waldron, Martin Morgan

Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Martin Morgan, Levi Waldron, Markus Riester