Pancreas (by batch)

Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq).

Raw Scaled

Rank	Name	Mean score	ARI	ARI	Graph connectivity	Graph connectivity	Isolated label F1	Isolated label F1	NMI	NMI	Memory (GB)	Runtime (min)	CPU (%)	Year	Library
1	Scanorama (hvg/unscaled)	0.96	0.96	0.96	1.00	0.99	0.95	0.95	0.93	0.93	3.80	2.40	538.90	2019	v1.7
2	scANVI (hvg/unscaled)	0.96	0.95	0.95	1.00	1.00	0.95	0.95	0.92	0.92	3.50	44.08	1,108.20	2021	v0.20.0
3	Scanorama (hvg/scaled)	0.95	0.95	0.95	0.99	0.99	0.95	0.95	0.92	0.92	5.10	7.08	441.20	2019	v1.7
4	Combat (hvg/scaled)	0.95	0.95	0.95	1.00	0.99	0.96	0.96	0.92	0.92	3.80	5.77	341.80	2007	v1.9.1
5	scANVI (full/unscaled)	0.95	0.95	0.95	1.00	1.00	0.95	0.94	0.92	0.92	4.90	116.77	2,042.40	2021	v0.20.0
6	MNN (hvg/scaled)	0.95	0.94	0.94	0.99	0.99	0.96	0.95	0.91	0.91	80.10	13.25	479.60	2018	v0.1.9.5
7	scVI (hvg/unscaled)	0.95	0.95	0.95	0.99	0.99	0.95	0.95	0.92	0.91	2.30	45.02	565.70	2018	v0.20.0
8	scVI (full/unscaled)	0.95	0.94	0.94	1.00	1.00	0.94	0.94	0.91	0.91	3.90	53.73	2,636.50	2018	v0.20.0
9	Harmony (hvg/unscaled)	0.94	0.94	0.94	0.99	0.99	0.93	0.93	0.92	0.92	2.10	1.63	351.60	2019	v0.1.7
10	Combat (hvg/unscaled)	0.94	0.94	0.94	1.00	0.99	0.93	0.92	0.91	0.91	3.20	6.25	205.20	2007	v1.9.1
11	Combat (full/unscaled)	0.94	0.95	0.95	0.99	0.99	0.89	0.89	0.92	0.92	13.80	3.07	561.90	2007	v1.9.1
12	BBKNN (hvg/scaled)	0.93	0.92	0.92	1.00	1.00	0.95	0.94	0.86	0.86	2.40	1.30	346.60	2020	v1.5.1
13	Scanorama (full/scaled)	0.93	0.91	0.91	0.99	0.99	0.96	0.95	0.87	0.87	30.80	15.25	878.20	2019	v1.7
14	BBKNN (hvg/unscaled)	0.92	0.95	0.95	1.00	1.00	0.85	0.84	0.90	0.90	2.00	3.20	455.00	2020	v1.5.1
15	MNN (hvg/unscaled)	0.91	0.85	0.85	1.00	0.99	0.93	0.93	0.88	0.88	35.80	5.40	1,169.80	2018	v0.1.9.5
16	SCALEX (hvg)	0.91	0.94	0.94	0.99	0.99	0.81	0.80	0.91	0.91	19.90	25.03	556.50	2022	v1.0.2
17	Harmony (full/unscaled)	0.90	0.91	0.91	0.99	0.99	0.84	0.83	0.87	0.87	2.50	6.30	283.60	2019	v0.1.7
18	BBKNN (full/unscaled)	0.90	0.91	0.91	1.00	0.99	0.85	0.84	0.86	0.86	2.90	6.40	218.10	2020	v1.5.1
19	FastMNN feature (hvg/scaled)	0.90	0.93	0.93	0.95	0.94	0.86	0.84	0.88	0.88	5.40	6.58	124.30	2019	v1.14.1
20	MNN (full/unscaled)	0.89	0.84	0.84	0.99	0.99	0.89	0.88	0.87	0.87	145.50	33.13	1,549.80	2018	v0.1.9.5
21	Harmony (hvg/scaled)	0.89	0.91	0.91	0.99	0.98	0.82	0.80	0.87	0.87	2.40	25.70	336.90	2019	v0.1.7
22	BBKNN (full/scaled)	0.89	0.83	0.83	1.00	0.99	0.96	0.95	0.78	0.78	7.50	5.05	254.40	2020	v1.5.1
23	Scanorama gene output (hvg/scaled)	0.89	0.77	0.77	0.99	0.99	0.95	0.95	0.84	0.84	5.40	4.07	716.70	2019	v1.7
24	Harmony (full/scaled)	0.88	0.83	0.83	0.99	0.98	0.92	0.92	0.81	0.81	7.50	11.83	509.50	2019	v0.1.7
25	FastMNN embed (hvg/unscaled)	0.87	0.84	0.84	0.95	0.94	0.86	0.84	0.84	0.84	3.00	3.33	94.10	2019	v1.14.1
26	SCALEX (full)	0.86	0.92	0.92	0.99	0.99	0.71	0.69	0.86	0.86	29.60	58.40	2,483.40	2022	v1.0.2
27	FastMNN embed (full/scaled)	0.86	0.88	0.88	0.96	0.95	0.81	0.79	0.83	0.83	10.40	10.17	99.10	2019	v1.14.1
28	FastMNN embed (hvg/scaled)	0.85	0.79	0.79	0.95	0.94	0.86	0.85	0.83	0.83	3.30	4.38	76.20	2019	v1.14.1
29	FastMNN embed (full/unscaled)	0.85	0.88	0.88	0.96	0.95	0.76	0.74	0.83	0.83	6.50	7.30	84.60	2019	v1.14.1
30	FastMNN feature (hvg/unscaled)	0.85	0.79	0.79	0.95	0.94	0.85	0.84	0.83	0.83	5.30	6.27	133.40	2019	v1.14.1
31	Scanorama gene output (hvg/unscaled)	0.85	0.66	0.66	0.99	0.98	0.92	0.92	0.83	0.83	4.70	9.70	413.20	2019	v1.7
32	FastMNN feature (full/unscaled)	0.84	0.89	0.89	0.96	0.95	0.71	0.69	0.84	0.84	18.00	7.25	120.30	2019	v1.14.1
33	FastMNN feature (full/scaled)	0.83	0.87	0.87	0.96	0.95	0.72	0.70	0.82	0.82	22.50	12.38	209.90	2019	v1.14.1
34	Scanorama gene output (full/scaled)	0.82	0.65	0.65	0.98	0.97	0.92	0.92	0.75	0.75	30.70	23.97	369.00	2019	v1.7
35	Scanorama (full/unscaled)	0.80	0.60	0.60	0.99	0.99	0.86	0.85	0.78	0.78	27.70	10.25	1,249.20	2019	v1.7
36	Scanorama gene output (full/unscaled)	0.79	0.61	0.61	0.99	0.99	0.80	0.79	0.76	0.76	27.70	6.80	1,478.00	2019	v1.7
37	MNN (full/scaled)	0.68	0.52	0.52	0.98	0.98	0.70	0.68	0.54	0.54	501.50	54.82	1,253.60	2018	v0.1.9.5
38	Combat (full/scaled)	0.63	0.39	0.39	0.94	0.93	0.75	0.73	0.47	0.47	15.80	10.27	340.80	2007	v1.9.1
39	Liger (hvg/unscaled)	0.51	0.38	0.38	0.75	0.69	0.64	0.61	0.38	0.38	3.70	37.12	101.00	2019	v0.5.0.9000
40	Liger (full/unscaled)	0.50	0.37	0.36	0.77	0.71	0.61	0.58	0.36	0.36	13.50	174.90	100.50	2019	v0.5.0.9000