HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

por Weber, Lukas M., Soneson, Charlotte
Publicado 2019

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

por Weber, Lukas M., Nowicka, Malgorzata, Soneson, Charlotte, Robinson, Mark D.
Publicado 2019

nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes

por Weber, Lukas M., Saha, Arkajyoti, Datta, Abhirup, Hansen, Kasper D., Hicks, Stephanie C.
Publicado 2023

Statistical methods for detecting differentially methylated loci and regions

por Robinson, Mark D., Kahraman, Abdullah, Law, Charity W., Lindsay, Helen, Nowicka, Malgorzata, Weber, Lukas M., Zhou, Xiaobei
Publicado 2014

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

por Hippen, Ariel A., Omran, Dalia K., Weber, Lukas M., Jung, Euihye, Drapkin, Ronny, Doherty, Jennifer A., Hicks, Stephanie C., Greene, Casey S.
Publicado 2023

Essential guidelines for computational method benchmarking

por Weber, Lukas M., Saelens, Wouter, Cannoodt, Robrecht, Soneson, Charlotte, Hapfelmeier, Alexander, Gardner, Paul P., Boulesteix, Anne-Laure, Saeys, Yvan, Robinson, Mark D.
Publicado 2019

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

por Weber, Lukas M, Hippen, Ariel A, Hickey, Peter F, Berrett, Kristofer C, Gertz, Jason, Doherty, Jennifer Anne, Greene, Casey S, Hicks, Stephanie C
Publicado 2021

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

por Nowicka, Malgorzata, Krieg, Carsten, Crowell, Helena L., Weber, Lukas M., Hartmann, Felix J., Guglietta, Silvia, Becher, Burkhard, Levesque, Mitchell P., Robinson, Mark D.
Publicado 2019

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

por Righelli, Dario, Weber, Lukas M, Crowell, Helena L, Pardo, Brenda, Collado-Torres, Leonardo, Ghazanfar, Shila, Lun, Aaron T L, Hicks, Stephanie C, Risso, Davide
Publicado 2022

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

por Hippen, Ariel A., Falco, Matias M., Weber, Lukas M., Erkan, Erdogan Pekcan, Zhang, Kaiyang, Doherty, Jennifer Anne, Vähärautio, Anna, Greene, Casey S., Hicks, Stephanie C.
Publicado 2021

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

por Pardo, Brenda, Spangler, Abby, Weber, Lukas M., Page, Stephanie C., Hicks, Stephanie C., Jaffe, Andrew E., Martinowich, Keri, Maynard, Kristen R., Collado-Torres, Leonardo
Publicado 2022

Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy

por Krieg, Carsten, Weber, Lukas M, Fosso, Bruno, Marzano, Marinella, Hardiman, Gary, Olcina, Monica M, Domingo, Enric, El Aidy, Sahar, Mallah, Khalil, Robinson, Mark D, Guglietta, Silvia
Publicado 2022

High-dimensional single-cell analysis reveals the immune signature of narcolepsy

por Hartmann, Felix J., Bernard-Valnet, Raphaël, Quériault, Clémence, Mrdjen, Dunja, Weber, Lukas M., Galli, Edoardo, Krieg, Carsten, Robinson, Mark D., Nguyen, Xuan-Hung, Dauvilliers, Yves, Liblau, Roland S., Becher, Burkhard
Publicado 2016

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

por Maynard, Kristen R., Collado-Torres, Leonardo, Weber, Lukas M., Uytingco, Cedric, Barry, Brianna K., Williams, Stephen R., Catallini, Joseph L., Tran, Matthew N., Besich, Zachary, Tippani, Madhavi, Chew, Jennifer, Yin, Yifeng, Kleinman, Joel E., Hyde, Thomas M., Rao, Nikhil, Hicks, Stephanie C., Martinowich, Keri, Jaffe, Andrew E.
Publicado 2021

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

por Petrillo, Mauro, Fabbri, Marco, Kagkli, Dafni Maria, Querci, Maddalena, Van den Eede, Guy, Alm, Erik, Aytan-Aktug, Derya, Capella-Gutierrez, Salvador, Carrillo, Catherine, Cestaro, Alessandro, Chan, Kok-Gan, Coque, Teresa, Endrullat, Christoph, Gut, Ivo, Hammer, Paul, Kay, Gemma L., Madec, Jean-Yves, Mather, Alison E., McHardy, Alice Carolyn, Naas, Thierry, Paracchini, Valentina, Peter, Silke, Pightling, Arthur, Raffael, Barbara, Rossen, John, Ruppé, Etienne, Schlaberg, Robert, Vanneste, Kevin, Weber, Lukas M., Westh, Henrik, Angers-Loustau, Alexandre
Publicado 2022