Best practices for single-cell analysis across modalities.
Journal
Nature reviews. Genetics
ISSN: 1471-0064
Titre abrégé: Nat Rev Genet
Pays: England
ID NLM: 100962779
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
accepted:
14
02
2023
medline:
19
7
2023
pubmed:
1
4
2023
entrez:
31
3
2023
Statut:
ppublish
Résumé
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
Identifiants
pubmed: 37002403
doi: 10.1038/s41576-023-00586-w
pii: 10.1038/s41576-023-00586-w
pmc: PMC10066026
doi:
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
550-572Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : K99 CA267677
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009937
Pays : United States
Investigateurs
Hananeh Aliee
(H)
Meshal Ansari
(M)
Pau Badia-I-Mompel
(P)
Maren Büttner
(M)
Emma Dann
(E)
Daniel Dimitrov
(D)
Leander Dony
(L)
Amit Frishberg
(A)
Dongze He
(D)
Soroor Hediyeh-Zadeh
(S)
Leon Hetzel
(L)
Ignacio L Ibarra
(IL)
Matthew G Jones
(MG)
Mohammad Lotfollahi
(M)
Laura D Martens
(LD)
Christian L Müller
(CL)
Mor Nitzan
(M)
Johannes Ostner
(J)
Giovanni Palla
(G)
Rob Patro
(R)
Zoe Piran
(Z)
Ciro Ramírez-Suástegui
(C)
Julio Saez-Rodriguez
(J)
Hirak Sarkar
(H)
Benjamin Schubert
(B)
Lisa Sikkema
(L)
Avi Srivastava
(A)
Jovan Tanevski
(J)
Isaac Virshup
(I)
Philipp Weiler
(P)
Informations de copyright
© 2023. Springer Nature Limited.
Références
Genome Biol. 2020 Dec 10;21(1):300
pubmed: 33303016
Nat Methods. 2022 Jan;19(1):41-50
pubmed: 34949812
Nat Biotechnol. 2021 May;39(5):619-629
pubmed: 33558698
Mol Cell. 2018 Sep 6;71(5):858-871.e8
pubmed: 30078726
Nat Commun. 2021 Oct 7;12(1):5890
pubmed: 34620862
BMC Genomics. 2018 Jun 19;19(1):477
pubmed: 29914354
Nat Methods. 2021 Jul;18(7):723-732
pubmed: 34155396
Genome Med. 2018 Mar 20;10(1):20
pubmed: 29558968
Bioinform Adv. 2022 Mar 08;2(1):vbac016
pubmed: 36699385
Nat Methods. 2019 May;16(5):397-400
pubmed: 30962623
Genes (Basel). 2021 Dec 02;12(12):
pubmed: 34946896
Nat Methods. 2021 Nov;18(11):1333-1341
pubmed: 34725479
Nat Methods. 2023 Sep;20(9):1355-1367
pubmed: 37443338
Nucleic Acids Res. 2021 Apr 19;49(7):e42
pubmed: 33524142
Nat Commun. 2021 Feb 2;12(1):738
pubmed: 33531494
Nat Methods. 2021 Jun;18(6):627-630
pubmed: 33986545
Science. 2016 Jul 1;353(6294):78-82
pubmed: 27365449
Nat Rev Mol Cell Biol. 2019 May;20(5):285-302
pubmed: 30659282
Nat Genet. 2021 Mar;53(3):403-411
pubmed: 33633365
Nature. 2018 Aug;560(7719):494-498
pubmed: 30089906
Cell. 2022 Jul 7;185(14):2559-2575.e28
pubmed: 35688146
Nat Methods. 2018 Aug;15(8):563-565
pubmed: 30065371
Science. 2015 Apr 24;348(6233):aaa6090
pubmed: 25858977
Nat Commun. 2022 Jan 21;13(1):440
pubmed: 35064122
Nat Biotechnol. 2022 Apr;40(4):476-479
pubmed: 34845373
Nat Biotechnol. 2022 Jan;40(1):121-130
pubmed: 34462589
Cell. 2019 Dec 12;179(7):1636-1646.e15
pubmed: 31787378
Cell. 2022 Mar 31;185(7):1223-1239.e20
pubmed: 35290801
Nat Biotechnol. 2017 Oct;35(10):936-939
pubmed: 28854175
NAR Genom Bioinform. 2022 Jul 13;4(3):lqac049
pubmed: 35855325
Bioinformatics. 2020 Aug 15;36(14):4137-4143
pubmed: 32353146
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
Trends Immunol. 2015 Nov;36(11):738-749
pubmed: 26508293
Bioinformatics. 2023 Jan 1;39(1):
pubmed: 36515467
Immunol Cell Biol. 2016 Mar;94(3):242-9
pubmed: 26606974
Nat Biotechnol. 2020 Dec;38(12):1408-1414
pubmed: 32747759
Genome Biol. 2021 Oct 29;22(1):301
pubmed: 34715899
Cell Syst. 2021 Aug 18;12(8):810-826.e4
pubmed: 34146472
Bioinformatics. 2021 Sep 9;37(17):2644-2650
pubmed: 33704427
Curr Protoc. 2022 Apr;2(4):e405
pubmed: 35384407
Trends Biotechnol. 2021 Jan;39(1):43-58
pubmed: 32505359
Nat Med. 2021 May;27(5):904-916
pubmed: 33879890
Nat Biotechnol. 2021 Oct;39(10):1202-1215
pubmed: 33941931
Nat Biotechnol. 2022 Jul;40(7):1066-1074
pubmed: 35190690
Nat Commun. 2021 Nov 25;12(1):6876
pubmed: 34824236
Genome Biol. 2019 Dec 23;20(1):295
pubmed: 31870412
Genome Biol. 2021 Sep 6;22(1):258
pubmed: 34488842
Nat Methods. 2020 Feb;17(2):159-162
pubmed: 31819264
Sci Adv. 2021 Apr 14;7(16):
pubmed: 33853780
Cell. 2019 Dec 12;179(7):1455-1467
pubmed: 31835027
Cell. 2016 Dec 15;167(7):1853-1866.e17
pubmed: 27984732
Nat Genet. 2021 Mar;53(3):322-331
pubmed: 33649593
Nat Biotechnol. 2021 Nov;39(11):1375-1384
pubmed: 34083791
Nat Methods. 2017 Sep;14(9):865-868
pubmed: 28759029
Bioessays. 2020 Oct;42(10):e1900221
pubmed: 32363691
Bioinformatics. 2021 Nov 18;37(22):4216-4226
pubmed: 34128955
Nat Commun. 2021 Feb 26;12(1):1337
pubmed: 33637727
Bioinformatics. 2011 Jun 15;27(12):1739-40
pubmed: 21546393
Nat Methods. 2021 Jan;18(1):92-99
pubmed: 33408405
Mol Syst Biol. 2023 Jun 12;19(6):e11517
pubmed: 37154091
Nat Biotechnol. 2019 May;37(5):547-554
pubmed: 30936559
Nat Methods. 2014 Apr;11(4):360-1
pubmed: 24681720
Nature. 2023 Sep;621(7978):365-372
pubmed: 36198796
Bioinformatics. 2020 Feb 1;36(3):897-903
pubmed: 31373607
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nat Methods. 2022 Feb;19(2):171-178
pubmed: 35102346
Nat Biotechnol. 2022 Feb;40(2):245-253
pubmed: 34594043
Nature. 2019 Feb;566(7745):490-495
pubmed: 30787436
Nat Methods. 2021 Jan;18(1):18-22
pubmed: 33408406
Nat Methods. 2020 Feb;17(2):193-200
pubmed: 31988518
Nature. 2017 Jul 6;547(7661):94-98
pubmed: 28636589
Cell Syst. 2021 Jun 16;12(6):522-537
pubmed: 34139164
Genome Biol. 2018 Feb 6;19(1):15
pubmed: 29409532
Bioinformatics. 2020 Sep 15;36(18):4817-4818
pubmed: 32614448
PLoS Comput Biol. 2022 Sep 12;18(9):e1010492
pubmed: 36094956
Nat Commun. 2022 Apr 19;13(1):2099
pubmed: 35440536
Front Genet. 2021 Dec 07;12:766405
pubmed: 34950190
Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692
pubmed: 34788843
Brief Bioinform. 2021 May 20;22(3):
pubmed: 32770205
Nat Methods. 2019 Dec;16(12):1226-1232
pubmed: 31570887
Nat Methods. 2023 Jan;20(1):86-94
pubmed: 36550277
STAR Protoc. 2021 Jul 28;2(3):100699
pubmed: 34382023
Genome Biol. 2019 Dec 23;20(1):296
pubmed: 31870423
Nature. 2015 Jul 23;523(7561):486-90
pubmed: 26083756
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Bioinformatics. 2016 Feb 15;32(4):587-9
pubmed: 26508757
Science. 2020 Jan 3;367(6473):45-51
pubmed: 31806696
Nat Methods. 2019 Dec;16(12):1289-1296
pubmed: 31740819
Nat Biotechnol. 2019 Dec;37(12):1482-1492
pubmed: 31796933
Mol Metab. 2020 Feb;32:109-121
pubmed: 32029221
Mol Biol Evol. 1987 Jul;4(4):406-25
pubmed: 3447015
Cell. 2021 Jun 24;184(13):3573-3587.e29
pubmed: 34062119
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Mol Syst Biol. 2022 Mar;18(3):e10798
pubmed: 35226415
Mol Syst Biol. 2021 Aug;17(8):e10282
pubmed: 34435732
Cell Rep. 2019 Oct 1;29(1):202-211.e6
pubmed: 31577949
Bioinformatics. 2022 May 26;38(11):3128-3131
pubmed: 35482478
Genome Biol. 2022 Feb 1;23(1):42
pubmed: 35105358
BMC Genomics. 2018 Mar 1;19(1):169
pubmed: 29490630
Nat Methods. 2015 May;12(5):380-1
pubmed: 25924071
Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427
pubmed: 28977646
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Cell. 2018 Jul 26;174(3):716-729.e27
pubmed: 29961576
Gigascience. 2020 Dec 26;9(12):
pubmed: 33367645
Nat Biotechnol. 2022 Mar;40(3):308-318
pubmed: 35132261
Methods Mol Biol. 2023;2584:269-292
pubmed: 36495456
Genome Biol. 2020 May 11;21(1):111
pubmed: 32393329
Genome Res. 2019 Aug;29(8):1363-1375
pubmed: 31340985
Nat Methods. 2022 Feb;19(2):179-186
pubmed: 35027765
Nat Biotechnol. 2022 May;40(5):661-671
pubmed: 35027729
Nat Biotechnol. 2019 Jun;37(6):685-691
pubmed: 31061482
Cell Syst. 2021 Feb 17;12(2):176-194.e6
pubmed: 33338399
Genome Biol. 2020 Apr 14;21(1):92
pubmed: 32290857
F1000Res. 2020 Jan 27;9:47
pubmed: 32789006
Nat Commun. 2021 Feb 17;12(1):1088
pubmed: 33597522
Bioinformatics. 2020 Jul 1;36(Suppl_1):i48-i56
pubmed: 32657382
Nat Methods. 2022 Sep;19(9):1097-1108
pubmed: 36068320
Bioinformatics. 2021 Oct 11;37(19):3243-3251
pubmed: 33970215
Nat Commun. 2019 Oct 11;10(1):4667
pubmed: 31604912
Nat Biotechnol. 2020 Jun;38(6):747-755
pubmed: 32518403
Nat Methods. 2018 Dec;15(12):1053-1058
pubmed: 30504886
Nat Methods. 2020 Feb;17(2):137-145
pubmed: 31792435
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361
pubmed: 27899662
Nat Methods. 2021 Mar;18(3):272-282
pubmed: 33589839
Genome Biol. 2022 Apr 14;23(1):97
pubmed: 35422018
Nat Methods. 2018 Apr;15(4):255-261
pubmed: 29481549
Nat Methods. 2022 Jun;19(6):662-670
pubmed: 35577954
Nat Biotechnol. 2023 Mar;41(3):332-336
pubmed: 36302986
Science. 2022 May 13;376(6594):eabl4290
pubmed: 35549429
Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):
pubmed: 34001664
Front Immunol. 2017 Mar 14;8:278
pubmed: 28352270
Nat Methods. 2023 Sep;20(9):1323-1335
pubmed: 37550580
PLoS Biol. 2018 Jul 3;16(7):e2005970
pubmed: 29969450
Nat Biotechnol. 2018 Jun;36(5):411-420
pubmed: 29608179
Nat Methods. 2013 Sep;10(9):857-60
pubmed: 23852452
J Immunol. 2019 Feb 1;202(3):637-644
pubmed: 30670579
Nat Methods. 2021 Nov;18(11):1352-1362
pubmed: 34711971
Cell Syst. 2019 Oct 23;9(4):383-392.e6
pubmed: 31521605
Science. 2015 May 22;348(6237):910-4
pubmed: 25953818
Comput Struct Biotechnol J. 2020 Jun 12;18:1429-1439
pubmed: 32637041
BMC Bioinformatics. 2019 Jan 18;20(1):40
pubmed: 30658573
Genome Biol. 2019 Sep 9;20(1):194
pubmed: 31500660
Comput Struct Biotechnol J. 2020 Oct 15;18:2953-2961
pubmed: 33209207
Nat Biotechnol. 2014 Jul;32(7):684-92
pubmed: 24952902
Genome Biol. 2020 Jan 16;21(1):12
pubmed: 31948481
Nat Protoc. 2021 Aug;16(8):3836-3873
pubmed: 34172974
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Nat Biotechnol. 2023 May 25;:
pubmed: 37231260
Cell Syst. 2021 Feb 17;12(2):128-140.e4
pubmed: 33373583
Nat Commun. 2021 Aug 16;12(1):4940
pubmed: 34400634
Nat Methods. 2017 Oct;14(10):975-978
pubmed: 28825706
Nat Methods. 2021 Jan;18(1):100-106
pubmed: 33318659
Nat Biotechnol. 2022 Jan;40(1):54-63
pubmed: 34426704
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Nat Biotechnol. 2018 Jan;36(1):70-80
pubmed: 29227469
Genome Biol. 2019 Nov 18;20(1):241
pubmed: 31739806
Nat Rev Genet. 2019 May;20(5):257-272
pubmed: 30696980
Sci Rep. 2020 Jun 23;10(1):10150
pubmed: 32576878
Nature. 2023 Feb;614(7949):742-751
pubmed: 36755098
Nat Commun. 2018 Jan 2;9(1):20
pubmed: 29295995
Nat Commun. 2019 May 20;10(1):2233
pubmed: 31110232
Nat Biotechnol. 2023 May 25;:
pubmed: 37231261
Nat Methods. 2019 Aug;16(8):715-721
pubmed: 31363220
Nature. 2022 Sep;609(7926):375-383
pubmed: 35978191
Genome Biol. 2020 Sep 1;21(1):227
pubmed: 32873325
Nat Biotechnol. 2022 Oct;40(10):1458-1466
pubmed: 35501393
Bioinformatics. 2017 Feb 1;33(3):425-427
pubmed: 28172415
Science. 2018 Sep 28;361(6409):1380-1385
pubmed: 30166440
Bioinformatics. 2020 Apr 1;36(7):2293-2294
pubmed: 31808789
Nucleic Acids Res. 2020 Oct 9;48(18):e107
pubmed: 32955565
Brief Bioinform. 2022 Sep 20;23(5):
pubmed: 35880426
Genome Biol. 2016 Apr 27;17:75
pubmed: 27122128
Nat Methods. 2021 Nov;18(11):1342-1351
pubmed: 34711970
Nat Methods. 2021 Jun;18(6):635-642
pubmed: 34059827
Genome Biol. 2021 Mar 8;22(1):78
pubmed: 33685491
Cell Rep Methods. 2022 Mar 15;2(3):100182
pubmed: 35475224
Sci Rep. 2019 Jun 27;9(1):9354
pubmed: 31249361
F1000Res. 2018 Aug 15;7:1297
pubmed: 30228881
BMC Bioinformatics. 2013 Jan 16;14:7
pubmed: 23323831
PLoS Comput Biol. 2023 Aug 17;19(8):e1011288
pubmed: 37590228
Comput Struct Biotechnol J. 2021 Jan 19;19:961-969
pubmed: 33613863
Nat Biotechnol. 2010 May;28(5):495-501
pubmed: 20436461
Nat Protoc. 2021 Jun;16(6):2749-2764
pubmed: 34031612
Nat Biotechnol. 2018 Nov 12;:
pubmed: 30418433
Nat Methods. 2022 Feb;19(2):159-170
pubmed: 35027767
Nat Biotechnol. 2022 Mar;40(3):345-354
pubmed: 34650268
Cell. 2019 Jul 25;178(3):714-730.e22
pubmed: 31348891
Sci Rep. 2019 Mar 26;9(1):5233
pubmed: 30914743
Nat Biomed Eng. 2020 Aug;4(8):827-834
pubmed: 32572199
F1000Res. 2018 Jul 26;7:1141
pubmed: 30271584
Genome Biol. 2019 Mar 19;20(1):59
pubmed: 30890159
BMC Bioinformatics. 2019 Dec 24;20(Suppl 19):721
pubmed: 31870280
Nat Methods. 2021 Jan;18(1):15-18
pubmed: 33408402
Nat Methods. 2023 May;20(5):665-672
pubmed: 37037999
Science. 2022 May 13;376(6594):eabl5197
pubmed: 35549406
Nat Commun. 2021 May 10;12(1):2593
pubmed: 33972535
Genome Biol. 2020 Mar 5;21(1):57
pubmed: 32138770
Nat Biotechnol. 2021 Jan;39(1):30-34
pubmed: 32690972
Nat Commun. 2021 Sep 28;12(1):5692
pubmed: 34584091
Nat Commun. 2019 Jan 28;10(1):470
pubmed: 30692544
Genome Biol. 2020 Feb 7;21(1):31
pubmed: 32033589
Nat Rev Genet. 2022 Dec;23(12):728-740
pubmed: 35831531
Nature. 2017 Jul 6;547(7661):89-93
pubmed: 28636592
F1000Res. 2021 Sep 28;10:979
pubmed: 35814628
Nat Protoc. 2018 Dec;13(12):2742-2757
pubmed: 30446749
Front Immunol. 2021 Apr 26;12:664514
pubmed: 33981311
Nat Commun. 2021 Jun 10;12(1):3545
pubmed: 34112806
Genome Biol. 2015 Dec 10;16:278
pubmed: 26653891
Front Immunol. 2021 Mar 11;12:640725
pubmed: 33777034
Nat Commun. 2020 Apr 29;11(1):2084
pubmed: 32350282
F1000Res. 2020 Apr 1;9:223
pubmed: 32765839
Mol Syst Biol. 2021 Jan;17(1):e9620
pubmed: 33491336
Genome Res. 2021 Oct;31(10):1706-1718
pubmed: 34599004
Cell Stem Cell. 2016 Aug 4;19(2):266-277
pubmed: 27345837
Mol Syst Biol. 2019 Jun 19;15(6):e8746
pubmed: 31217225
Nat Methods. 2018 May;15(5):343-346
pubmed: 29553579
Genome Biol. 2021 Sep 1;22(1):252
pubmed: 34465366
Nat Biotechnol. 2022 Apr;40(4):517-526
pubmed: 33603203
Development. 2019 Jun 27;146(12):
pubmed: 31249005
Nat Methods. 2018 Feb;15(2):123-126
pubmed: 29309061
Nat Protoc. 2020 Apr;15(4):1484-1506
pubmed: 32103204
Genome Biol. 2022 Jan 31;23(1):41
pubmed: 35101061
Nat Commun. 2022 Jun 9;13(1):3224
pubmed: 35680885
Nat Biotechnol. 2021 Oct;39(10):1246-1258
pubmed: 34083792
J Comput Biol. 2022 Jan;29(1):3-18
pubmed: 35050714
Nat Rev Genet. 2015 Jan;16(1):57-66
pubmed: 25446315
Nat Methods. 2017 Jun;14(6):565-571
pubmed: 28504683
Nat Methods. 2023 Aug;20(8):1222-1231
pubmed: 37386189
Genome Biol. 2021 May 10;22(1):145
pubmed: 33971932
F1000Res. 2020 Dec 10;9:1444
pubmed: 33604029
Nucleic Acids Res. 2020 Jun 4;48(10):e55
pubmed: 32196115
Cell Genom. 2022 Sep 14;2(9):
pubmed: 36204155
Genome Biol. 2020 Feb 12;21(1):36
pubmed: 32051003
Immunity. 2022 Oct 11;55(10):1940-1952.e5
pubmed: 36223726