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.

5k Peripheral blood mononuclear cells

Rankroot mean squared errorlocal propertytrustworthinessco-KNN AUClocal continuity meta criterionglobal propertyco-KNN sizedensity preservationcontinuityMemory (GB)Runtime (min)CPU (%)NamePaperCodeYear
827.750.450.840.750.040.880.040.380.800.470.19164.50Principle Component Analysis (PCA) (logCPM, 1kHVG)

v1.1.2

1901
139.080.500.870.750.070.850.080.770.860.891.53105.70densMAP PCA (logCPM, 1kHVG)

v0.5.3

2021
343.560.480.870.740.070.850.08-0.000.810.792.4849.40Uniform Manifold Approximation and Projection (UMAP), as implemented by scanpy (logCPM, 1kHVG)

v0.5.3

2018
7580.300.370.890.690.060.780.060.340.710.751.77386.60PHATE (default)

v1.0.8

2019
550.640.450.860.740.060.860.070.100.790.781.75371.70PHATE (logCPM, 1kHVG)

v1.0.8

2019
641.500.450.820.720.060.830.070.740.860.932.38120.00densMAP (logCPM, 1kHVG)

v0.5.3

2021
9580.270.360.890.670.060.750.060.280.650.786.57659.00PHATE (gamma=0)

v1.0.8

2019
423.480.460.890.730.090.840.100.100.840.796.47220.60“t-Distributed Stochastic Neighbor Embedding (t-SNE) (logCPM, 1kHVG)

v0.1

2008
10491.790.370.890.670.040.760.040.480.702.709.752,061.00NeuralEE (CPU) (Default)

v0.1.6

2020
249.070.500.850.760.050.880.060.510.870.8729.82919.90NeuralEE (CPU) (logCPM, 1kHVG)

v0.1.6

2020