2022-Wang et al-preprint
Posted: Thu Apr 28, 2022 4:01 pm"A Comparison of Dimension Reduction Methods for Cytometry by Time-of-Flight Data"
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song, Xinlei Wang, Tao Wang
bioRxiv, posted April 27, 2022
https://doi.org/10.1101/2022.04.26.489549
- will update when/if this is peer-reviewed and published
- "Here, we benchmark 20 of these methods on 110 real and 425 synthetic CyTOF datasets, including 10 Imaging CyTOF datasets, for accuracy, scalability and usability."
- "For simulation of CyTOF data, we developed Cytomulate (method section), the first formal simulation tool that is able to well mimic the behaviors of CyTOF data."
- Note: these appear to be 110 real *files*; they are tied to 11 different *datasets*
TuPro: 2020-Stark et al-preprint/2020-Stark et al-Bioinformatics
Oetjen: 2018-Oetjen et al-preprint/2018-Oetjen et al-JCI Insight
CyAnno: 2020-Kaushik et al-preprint/2021-Kaushik et al-Bioinformatics
LG: 2017-Hawley et al-PLoS One
Brain: 2019-Böttcher et al-Nat Neurosci
BC: 2020-Jackson et al-Nature; IMC
Levine32: 2015-Levine et al-Cell
Levine13: 2015-Levine et al-Cell
Samusik: 2016-Samusik et al-Nat Methods
Lung cancer: 2021-Gonugunta et al-J Immunother Cancer ("Please request from data generating authors")
Covid- this paper: Database for Actionable Immunology https://dbai.biohpc.swmed.edu/cytof-database.php
- DR methods:
PCA
ICA
FA
ZIFA
SAUCIE
FIt-SNE
UMAP
Diffusion Map
scvis
scvis (Full)
MDS
LLE
Spectral
Kernel PCA: Poly
Kernel PCA: RBF
Isomap
PHATE
BH t-SNE
NMF
GrandPrix
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song, Xinlei Wang, Tao Wang
bioRxiv, posted April 27, 2022
https://doi.org/10.1101/2022.04.26.489549
- will update when/if this is peer-reviewed and published
- "Here, we benchmark 20 of these methods on 110 real and 425 synthetic CyTOF datasets, including 10 Imaging CyTOF datasets, for accuracy, scalability and usability."
- "For simulation of CyTOF data, we developed Cytomulate (method section), the first formal simulation tool that is able to well mimic the behaviors of CyTOF data."
- Note: these appear to be 110 real *files*; they are tied to 11 different *datasets*
TuPro: 2020-Stark et al-preprint/2020-Stark et al-Bioinformatics
Oetjen: 2018-Oetjen et al-preprint/2018-Oetjen et al-JCI Insight
CyAnno: 2020-Kaushik et al-preprint/2021-Kaushik et al-Bioinformatics
LG: 2017-Hawley et al-PLoS One
Brain: 2019-Böttcher et al-Nat Neurosci
BC: 2020-Jackson et al-Nature; IMC
Levine32: 2015-Levine et al-Cell
Levine13: 2015-Levine et al-Cell
Samusik: 2016-Samusik et al-Nat Methods
Lung cancer: 2021-Gonugunta et al-J Immunother Cancer ("Please request from data generating authors")
Covid- this paper: Database for Actionable Immunology https://dbai.biohpc.swmed.edu/cytof-database.php
- DR methods:
PCA
ICA
FA
ZIFA
SAUCIE
FIt-SNE
UMAP
Diffusion Map
scvis
scvis (Full)
MDS
LLE
Spectral
Kernel PCA: Poly
Kernel PCA: RBF
Isomap
PHATE
BH t-SNE
NMF
GrandPrix