batch_effect_pitfalls_n_methods.xlsx

	A	B	C	D	E
1	Method	Link	GNN	Category	N. methods

2	stLearn	https://www.biorxiv.org/content/10.1101/2020.05.31.125658v1	mag-20	Other	1
3	MERINGUE	https://genome.cshlp.org/content/31/10/1843	mag-21	Other	2
4	SEDR	https://www.biorxiv.org/content/10.1101/2021.06.15.448542v2	giu-21	GNN	3
5	BayesSpace	https://www.nature.com/articles/s41587-021-00935-2	giu-21	HMRF	4
6	MULTILAYER	https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00151-4	lug-21	Other	5
7	SpaGCN	SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network \| Nature Methods	ott-21	GNN	6
8	ClusterMap	https://www.nature.com/articles/s41467-021-26044-x	ott-21	Other	7
9	conST	https://www.biorxiv.org/content/10.1101/2022.01.14.476408v1	gen-22	Other	8
10	scMEB	https://academic.oup.com/bib/article-abstract/23/1/bbab466/6440124	gen-22	Other	9
11	MAPLE	https://www.biorxiv.org/content/10.1101/2022.02.28.482296v2.full	mar-22	Other	10
12	spatialGE	https://doi.org/10.1093/bioinformatics/btac145	mar-22	Other	11
13	STAGATE	https://www.nature.com/articles/s41467-022-29439-6	apr-22	GNN	12
14	CCST	https://www.nature.com/articles/s43588-022-00266-5	giu-22	GNN	13
15	DR-SC	https://academic.oup.com/nar/article/50/12/e72/6555431	lug-22	HMRF	14
16	SpaceFlow	https://www.nature.com/articles/s41467-022-31739-w	lug-22	GNN	15
17	Stardust	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9364686/	lug-22	Other	16
18	BASS	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02734-7	ago-22	Other	17
19	RESEPT	https://www.sciencedirect.com/science/article/pii/S2001037022003646	ago-22	GNN	18
20	ConGI	https://www.biorxiv.org/content/10.1101/2022.09.30.510297v1	ott-22	Other	19
21	SCAN-IT	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9552951/	ott-22	GNN	20
22	SOTIP	https://www.nature.com/articles/s41467-022-34867-5	nov-22	Other	21
23	SpatialPCA	https://www.nature.com/articles/s41467-022-34879-1	nov-22	Other	22
24	DeepST	https://academic.oup.com/nar/article/50/22/e131/6761985	dic-22	GNN	23
25	PRECAST	https://www.nature.com/articles/s41467-023-35947-w	gen-23	HMRF	24
26	SPICEMIX	https://www.nature.com/articles/s41588-022-01256-z	gen-23	HMRF	25
27	SpatialAnno	https://www.biorxiv.org/content/10.1101/2023.02.08.527590v1.full	feb-23	HMRF	26
28	GraphST	https://www.nature.com/articles/s41467-023-36796-3	mar-23	GNN	27
29	SECE	https://www.mdpi.com/2218-273X/14/6/674	mag-23	GNN	28
30	SpaSEG	https://www.biorxiv.org/content/10.1101/2022.11.16.516728v2.full	mag-23	Other	29
31	CLARIFY	https://academic.oup.com/bioinformatics/article/39/Supplement_1/i484/7210503	giu-23	GNN	30
32	Spatial MGCN	https://academic.oup.com/bib/article-abstract/24/5/bbad262/7225995?redirectedFrom=fulltext	lug-23	GNN	31
33	GASTON	https://www.biorxiv.org/content/10.1101/2023.10.10.561757v1.full	ott-23	Other	32
34	NeST	https://www.nature.com/articles/s41467-023-42343-x	ott-23	Other	33
35	SPIRAL	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03078-6	ott-23	GNN	34
36	PAST	https://genome.cshlp.org/content/33/10/1757.short	ott-23	Other	35
37	REGNN	https://www.biorxiv.org/content/10.1101/2023.11.09.566479v1.full	nov-23	GNN	36
38	SPACEL	https://www.nature.com/articles/s41467-023-43220-3	nov-23	GNN	37
39	hexCNN	https://www.sciencedirect.com/science/article/pii/S1046202323001846	nov-23	Other	38
40	ConSpaS	https://academic.oup.com/bib/article/24/6/bbad395/7420493	nov-23	GNN	39
41	BNPSpace	https://arxiv.org/abs/2312.08324	dic-23	HMRF	40
42	vGraphST	https://ieeexplore.ieee.org/abstract/document/10385692	dic-23	GNN	41
43	CellCharter	https://www.nature.com/articles/s41588-023-01588-4	dic-23	Other	42
44	CytoCommunity	https://www.nature.com/articles/s41592-023-02124-2	gen-24	Other	43
45	MENDER	https://www.nature.com/articles/s41467-023-44367-9	gen-24	Other	44
46	STAIG	https://www.biorxiv.org/content/10.1101/2023.12.18.572279v2.full	gen-24	GNN	45
47	GSG	https://www.researchsquare.com/article/rs-3583635/v1	gen-24	GNN	46
48	PROST	https://www.nature.com/articles/s41467-024-44835-w	gen-24	Other	47
49	GRAPHDeep	https://academic.oup.com/bioinformatics/article/40/1/btae023/7577854	gen-24	GNN	48
50	stAA	https://academic.oup.com/bib/article/25/1/bbad500/7512648	gen-24	GNN	49
51	SGCAST	https://academic.oup.com/bib/article/25/1/bbad490/7505237	gen-24	GNN	50
52	BANKSY	https://www.nature.com/articles/s41588-024-01664-3	feb-24	Other	51
53	STCC	https://www.biorxiv.org/content/10.1101/2024.02.25.581996v1.full	feb-24	Other	52
54	stMMR	https://www.biorxiv.org/content/biorxiv/early/2024/02/29/2024.02.22.581503.full	feb-24	GNN	53
55	BiGATAE	https://academic.oup.com/bib/article/25/2/bbae045/7611934	feb-24	GNN	54
56	SGAE	https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giae003/7610489	feb-24	GNN	55
57	SpacAE	https://academic.oup.com/bib/article/25/2/bbae016/7601764?login=false	mar-24	GNN	56
58	AVGN	https://academic.oup.com/bib/article/25/3/bbae173/7646266	mag-24	GNN	57
59	DenoiseST	https://www.biorxiv.org/content/10.1101/2024.03.04.583438v1.abstract	mag-24	GNN	58
60	GRAS4T	https://www.biorxiv.org/content/10.1101/2024.05.09.593192v2.abstract	mag-24	GNN	59
61	HyperSTAR	https://www.biorxiv.org/content/10.1101/2024.05.15.594168v1.abstract	mag-24	GNN	60
62	MNMST	https://link.springer.com/article/10.1186/s13059-024-03272-0	mag-24	Other	61
63	Path-MGCN	https://www.researchsquare.com/article/rs-4481813/v1	mag-24	GNN	62
64	PearlST	https://spj.science.org/doi/full/10.34133/research.0390	mag-24	GNN	63
65	STew	https://academic.oup.com/bioinformaticsadvances/article/4/1/vbae064/7684964	mag-24	Other	64
66	BINARY	https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00131-9	giu-24	GNN	65
67	iIMPACT	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03289-5	giu-24	HMRF	66
68	IRIS	https://www.nature.com/articles/s41592-024-02284-9	giu-24	Other	67
69	PRESENT	https://www.biorxiv.org/content/10.1101/2024.06.10.598155v1.abstract	giu-24	GNN	68
70	stMASK	https://www.biorxiv.org/content/10.1101/2024.05.30.596562v1.abstract	giu-24	GNN	69
71	BNPMFA	https://arxiv.org/abs/2408.14410	lug-24	HMRF	70
72	DeepDomain	https://link.springer.com/chapter/10.1007/978-981-97-5689-6_27	lug-24	GNN	71
73	DiffusionST	https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4894131	lug-24	GNN	72
74	mclSTExp	https://arxiv.org/abs/2407.08216	lug-24	Other	73
75	stCluster	https://academic.oup.com/bib/article-abstract/25/4/bbae329/7709092	lug-24	GNN	74
76	stMCFN	https://link.springer.com/chapter/10.1007/978-981-97-5689-6_28	lug-24	GNN	75
77	XVGAE	https://www.biorxiv.org/content/10.1101/2024.07.25.605067v1.abstract	lug-24	GNN	76
78	SpaNCMG	https://academic.oup.com/bib/article/25/4/bbae259/7684612	lug-24	GNN	77
79	stDGCC	https://academic.oup.com/bioinformatics/article/40/7/btae451/7714691?login=true	lug-24	GNN	78
80	stDyer	https://www.researchsquare.com/article/rs-4614224/v1	lug-24	GNN	79
81	stMDA	https://academic.oup.com/bib/article/25/4/bbae257/7685749	lug-24	GNN	80
82	HERGAST	https://www.biorxiv.org/content/10.1101/2024.08.09.607422v1.abstract	ago-24	GNN	81
83	SpaTopic	https://doi.org/10.1126/sciadv.adp4942	set-24	Other	82
84	SpaGCAC	https://doi.org/10.1109/TCBB.2024.3469164	set-24	Other	83
85	mosna	https://doi.org/10.1101/2023.03.16.532947	set-24	Other	84
86	Novae	https://doi.org/10.1101/2024.09.09.612009	set-24	GNN	85
87	SpaMNN	https://doi.org/10.1101/2024.10.08.615307	ott-24	Other	86
88	SpaGRA	https://doi.org/10.1016/j.jgg.2024.09.015	ott-24	GNN	87
89	STAGUE	https://doi.org/10.1002/advs.202403572	ott-24	GNN	88
90	MILWRM	https://doi.org/10.1038/s42003-024-06281-8	ott-24	Other	89
91	SDUCL	https://doi.org/10.1093/bioinformatics/btae663	nov-24	GNN	90
92	GraphCVAE	https://doi.org/10.1016/j.lfs.2024.123208	dic-24	GNN	91
93	SpaInGNN	https://doi.org/10.1016/j.ymeth.2024.11.006	gen-25	GNN	92
94	GAAEST	https://doi.org/10.1038/s42003-024-07037-0	gen-25	GNN	93
95
96	Data used in https://www.batcheffect.com/p/the-pitfalls-of-spatial-domain-identification
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