Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: diffcyt
https://packages.ecosyste.ms/registries/bioconductor.org/packages/diffcyt
Differential discovery in high-dimensional cytometry via high-resolution clustering
1 version
Latest release: about 1 year ago
4 dependent packages
21,519 downloads total
Papers Mentioning diffcyt 18
10.1186/s12859-021-04054-2
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry dataCited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: over 3 years ago
10.12688/f1000research.11622.3
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasetsCited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago
10.7554/eLife.62915
ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry dataCited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: over 3 years ago
10.1038/s42003-019-0415-5
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clusteringCited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 5 years ago
10.1186/s13059-021-02368-1
treeclimbR pinpoints the data-dependent resolution of hierarchical hypothesesCited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago
10.1186/s13059-021-02363-6
Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathwaysCited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: over 3 years ago
10.1186/s12859-021-04125-4
Censcyt: censored covariates in differential abundance analysis in cytometryCited by: 0
Author(s): Reto Gerber, Mark D. Robinson
Software Mentions: 8
Published: over 3 years ago
10.3389/fimmu.2021.634127
Immunophenotyping of Peripheral Blood Mononuclear Cells in Septic Shock Patients With High-Dimensional Flow Cytometry Analysis Reveals Two Subgroups With Differential Responses to Immunostimulant DrugsCited by: 4
Author(s): Ya Wang, Brian Gloss, Benjamin Tang, Suat Dervish, Brigitte Santner-Nanan, Christina Whitehead, Kristy Masters, Kristen K. Skarratt, Sally Teoh, Stephen D. Schibeci, Nicole Fewings, Chrystelle Brignone, Frédéric Triebel, David R. Booth, Anthony S. McLean, Marek Nalos
Software Mentions: 7
Published: over 3 years ago
10.3389/fimmu.2020.00714
Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass CytometryCited by: 7
Author(s): Thanmayi Ranganath, Laura J. Simpson, Anne-Maud Ferreira, Christof Seiler, Elena Vendrame, Nancy Q. Zhao, Jason D. Fontenot, Susan Holmes, Catherine A. Blish
Software Mentions: 6
Published: over 4 years ago
10.1186/s40478-020-01010-8
Single-cell mass cytometry reveals complex myeloid cell composition in active lesions of progressive multiple sclerosisCited by: 34
Author(s): Chotima Böttcher, Marlijn van der Poel, Camila Fernández-Zapata, Stephan Schlickeiser, Julia Koehler Leman, Cheng-Chih Hsiao, Mark R. Mizee, Adelia, Maria C. J. Vincenten, Désirée Kunkel, Inge Huitinga, Jörg Hamann, Josef Priller
Software Mentions: 5
Published: over 4 years ago
10.1186/s12859-021-04067-x
CytoGLMM: conditional differential analysis for flow and mass cytometry experimentsCited by: 13
Author(s): Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan Holmes
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2020.00829
Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer CellsCited by: 8
Author(s): Nancy Q. Zhao, Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish
Software Mentions: 4
Published: over 4 years ago
10.1038/s41598-019-55852-x
Multi-parameter immune profiling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosisCited by: 34
Author(s): Chotima Böttcher, Camila Fernández-Zapata, Stephan Schlickeiser, Désirée Kunkel, Axel Schulz, Henrik E. Mei, Carl Weidinger, René M. Gieß, Susanna Asseyer, Britta Siegmund, Friedemann Paul, Klemens Ruprecht, Josef Priller
Software Mentions: 4
Published: almost 5 years ago
10.15252/emmm.202013001
Altered bioenergetics and mitochondrial dysfunction of monocytes in patients with COVID‐19 pneumoniaCited by: 113
Author(s): Lara Gibellini, Sara De Biasi, Annamaria Paolini, Rebecca Borella, Federica Boraldi, Marco Mattioli, Domenico Lo Tartaro, Lucia Fidanza, Alfredo Caro‐Maldonado, Marianna Meschiari, Vittorio Iadisernia, Erica Bacca, Giovanni Riva, Luca Cicchetti, Daniela Quaglino, Giovanni Guaraldi, Stefano Busani, Massimo Girardis, Cristina Mussini, Andrea Cossarizza
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0238347
Natural killer cell phenotype is altered in HIV-exposed seronegative womenCited by: 15
Author(s): Nancy Q. Zhao, Elena Vendrame, Anne-Maud Ferreira, Christof Seiler, Thanmayi Ranganath, Michel Alary, Annie‐Claude Labbé, Fernand Guédou, Johanne Poudrier, Susan Holmes, Michel Roger, Catherine A. Blish
Software Mentions: 3
Published: about 4 years ago
10.3389/fimmu.2021.656846
Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney TransplantationCited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: over 3 years ago
10.7554/eLife.59630
Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasetsCited by: 25
Author(s): Marie Trussart, Charis E. Teh, Tania Tan, Lawrence Leong, Daniel H.D. Gray, Terence P. Speed
Software Mentions: 2
Published: about 4 years ago
10.1186/s12859-020-03671-7
Model-based clustering for flow and mass cytometry data with clinical informationCited by: 3
Author(s): Kayoko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura
Software Mentions: 2
Published: about 4 years ago