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: 10 months 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 data
Cited 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 datasets
Cited 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: about 5 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited 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: about 3 years ago

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: about 5 years ago

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: about 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 pathways
Cited 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: about 3 years ago

10.1186/s12859-021-04125-4

Censcyt: censored covariates in differential abundance analysis in cytometry
Cited by: 0
Author(s): Reto Gerber, Mark D. Robinson
Software Mentions: 8
Published: about 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 Drugs
Cited 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 Cytometry
Cited 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 sclerosis
Cited 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: almost 4 years ago

10.1186/s12859-021-04067-x

CytoGLMM: conditional differential analysis for flow and mass cytometry experiments
Cited 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 Cells
Cited by: 8
Author(s): Nancy Q. Zhao, Anne-Maud Ferreira, Philip Grant, Susan Holmes, Catherine A. Blish
Software Mentions: 4
Published: about 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 sclerosis
Cited 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: over 4 years ago

10.15252/emmm.202013001

Altered bioenergetics and mitochondrial dysfunction of monocytes in patients with COVID‐19 pneumonia
Cited 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: over 3 years ago

10.1371/journal.pone.0238347

Natural killer cell phenotype is altered in HIV-exposed seronegative women
Cited 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: almost 4 years ago

10.3389/fimmu.2021.656846

Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney Transplantation
Cited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.59630

Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets
Cited by: 25
Author(s): Marie Trussart, Charis E. Teh, Tania Tan, Lawrence Leong, Daniel H.D. Gray, Terence P. Speed
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-020-03671-7

Model-based clustering for flow and mass cytometry data with clinical information
Cited by: 3
Author(s): Kayoko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa, Teppei Shimamura
Software Mentions: 2
Published: almost 4 years ago