5k Peripheral blood mononuclear cells

5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics.

Rank	root mean squared error	local property	trustworthiness	co-KNN AUC	local continuity meta criterion	global property	co-KNN size	density preservation	continuity	Memory (GB)	Runtime (min)	CPU (%)	Name	Code	Year
8	27.75	0.45	0.84	0.75	0.04	0.88	0.04	0.38	0.80	0.47	0.19	164.50	Principle Component Analysis (PCA) (logCPM, 1kHVG)	v1.1.2	1901
1	39.08	0.50	0.87	0.75	0.07	0.85	0.08	0.77	0.86	0.89	1.53	105.70	densMAP PCA (logCPM, 1kHVG)	v0.5.3	2021
3	43.56	0.48	0.87	0.74	0.07	0.85	0.08	-0.00	0.81	0.79	2.48	49.40	Uniform Manifold Approximation and Projection (UMAP), as implemented by scanpy (logCPM, 1kHVG)	v0.5.3	2018
7	580.30	0.37	0.89	0.69	0.06	0.78	0.06	0.34	0.71	0.75	1.77	386.60	PHATE (default)	v1.0.8	2019
5	50.64	0.45	0.86	0.74	0.06	0.86	0.07	0.10	0.79	0.78	1.75	371.70	PHATE (logCPM, 1kHVG)	v1.0.8	2019
6	41.50	0.45	0.82	0.72	0.06	0.83	0.07	0.74	0.86	0.93	2.38	120.00	densMAP (logCPM, 1kHVG)	v0.5.3	2021
9	580.27	0.36	0.89	0.67	0.06	0.75	0.06	0.28	0.65	0.78	6.57	659.00	PHATE (gamma=0)	v1.0.8	2019
4	23.48	0.46	0.89	0.73	0.09	0.84	0.10	0.10	0.84	0.79	6.47	220.60	“t-Distributed Stochastic Neighbor Embedding (t-SNE) (logCPM, 1kHVG)	v0.1	2008
10	491.79	0.37	0.89	0.67	0.04	0.76	0.04	0.48	0.70	2.70	9.75	2,061.00	NeuralEE (CPU) (Default)	v0.1.6	2020
2	49.07	0.50	0.85	0.76	0.05	0.88	0.06	0.51	0.87	0.87	29.82	919.90	NeuralEE (CPU) (logCPM, 1kHVG)	v0.1.6	2020