Single Cell Atlas: a single-cell multi-omics human cell encyclopedia.
Flow cytometry
Human database
Mass cytometry
Multi-omics
Single Cell Atlas
Single-cell ATAC-sequencing
Single-cell RNA-sequencing
Single-cell immune profiling
Single-cell omics
Spatial transcriptomics
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
19 Apr 2024
19 Apr 2024
Historique:
received:
16
11
2022
accepted:
12
04
2024
medline:
20
4
2024
pubmed:
20
4
2024
entrez:
19
4
2024
Statut:
epublish
Résumé
Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of human tissues through in-depth characterizations of datasets from five single-cell omics, spatial transcriptomics, and two bulk omics across 125 healthy adult and fetal tissues. We construct its complement web-based platform, the Single Cell Atlas (SCA, www.singlecellatlas.org ), to enable vast interactive data exploration of deep multi-omics signatures across human fetal and adult tissues. The atlas resources and database queries aspire to serve as a one-stop, comprehensive, and time-effective resource for various omics studies.
Identifiants
pubmed: 38641842
doi: 10.1186/s13059-024-03246-2
pii: 10.1186/s13059-024-03246-2
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
104Subventions
Organisme : Karolinska Institutet
ID : C62623013
Organisme : Karolinska Institutet
ID : C24401073
Organisme : Karolinska Institutet
ID : C331612602
Informations de copyright
© 2024. The Author(s).
Références
Aldridge S, Teichmann SA. Single cell transcriptomics comes of age. Nat Commun. 2020;11:4307.
pubmed: 32855414
pmcid: 7453005
doi: 10.1038/s41467-020-18158-5
Zhu C, Preissl S, Ren B. Single-cell multimodal omics: the power of many. Nat Methods. 2020;17:11–4.
pubmed: 31907462
doi: 10.1038/s41592-019-0691-5
Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, Luo W, Huang T-S, Yeung BZ, Papalexi E, et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021;39:1246–58.
pubmed: 34083792
pmcid: 8763625
doi: 10.1038/s41587-021-00927-2
Li X. Harnessing the potential of spatial multiomics: a timely opportunity. Signal Transduct Target Ther. 2023;8:234.
pubmed: 37302998
pmcid: 10258193
doi: 10.1038/s41392-023-01507-3
Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Gerós AS, Gupta T, Ashley N, Khamis D, Fowler D, Morrissey E, et al. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell. 2021;184:810-826.e823.
pubmed: 33406409
pmcid: 7864098
doi: 10.1016/j.cell.2020.12.016
Miao Z, Humphreys BD, McMahon AP, Kim J. Multi-omics integration in the age of million single-cell data. Nat Rev Nephrol. 2021;17:710–24.
pubmed: 34417589
pmcid: 9191639
doi: 10.1038/s41581-021-00463-x
Chappell L, Russell AJC, Voet T. Single-Cell (Multi)omics Technologies. Annu Rev Genomics Hum Genet. 2018;19:15–41.
pubmed: 29727584
doi: 10.1146/annurev-genom-091416-035324
Li H, Qu L, Yang Y, Zhang H, Li X, Zhang X. Single-cell transcriptomic architecture unraveling the complexity of tumor heterogeneity in distal cholangiocarcinoma. Cell Mol Gastroenterol Hepatol. 2022;13(1592–1609): e1599.
Li M, Zhang X, Ang KS, Ling J, Sethi R, Lee NYS, Ginhoux F, Chen J. DISCO: a database of Deeply Integrated human Single-Cell Omics data. Nucleic Acids Res. 2022;50:D596-d602.
pubmed: 34791375
doi: 10.1093/nar/gkab1020
Pan L, Mou T, Huang Y, Hong W, Yu M, Li X. Ursa: A comprehensive multiomics toolbox for high-throughput single-cell analysis. Mol Biol Evol. 2023;40(12):msad267.
Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, et al. The Human Cell Atlas eLife. 2017;6: e27041.
pubmed: 29206104
Clough E, Barrett T. The gene expression omnibus database. Statistical Genomics: Methods and Protocols. 2016:93–110.
Franzén O, Gan L-M, Björkegren JLM: PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database 2019, 2019.
Cummins C, Ahamed A, Aslam R, Burgin J, Devraj R, Edbali O, Gupta D, Harrison PW, Haseeb M, Holt S, et al. The European Nucleotide Archive in 2021. Nucleic Acids Res. 2022;50:D106-d110.
pubmed: 34850158
doi: 10.1093/nar/gkab1051
Pan L, Shan S, Tremmel R, Li W, Liao Z, Shi H, Chen Q, Zhang X, Li X. HTCA: a database with an in-depth characterization of the single-cell human transcriptome. Nucleic Acids Res. 2022;51:D1019–28.
pmcid: 9825435
doi: 10.1093/nar/gkac791
Elmentaite R, Domínguez Conde C, Yang L, Teichmann SA. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet. 2022;23:395–410.
pubmed: 35217821
doi: 10.1038/s41576-022-00449-w
Quake SR: A decade of molecular cell atlases. Trends in Genetics 2022.
Zeng J, Zhang Y, Shang Y, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, et al. CancerSCEM: a database of single-cell expression map across various human cancers. Nucleic Acids Res. 2022;50:D1147-d1155.
pubmed: 34643725
doi: 10.1093/nar/gkab905
Ner-Gaon H, Melchior A, Golan N, Ben-Haim Y, Shay T. JingleBells: A Repository of Immune-Related Single-Cell RNA-Sequencing Datasets. J Immunol. 2017;198:3375–9.
pubmed: 28416714
doi: 10.4049/jimmunol.1700272
Tarhan L, Bistline J, Chang J, Galloway B, Hanna E, Weitz E: Single Cell Portal: an interactive home for single-cell genomics data. bioRxiv 2023.
Kolodziejczyk Aleksandra A, Kim JK, Svensson V, Marioni John C, Teichmann Sarah A. The Technology and Biology of Single-Cell RNA Sequencing. Mol Cell. 2015;58:610–20.
pubmed: 26000846
doi: 10.1016/j.molcel.2015.04.005
Schwartzman O, Tanay A. Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet. 2015;16:716–26.
pubmed: 26460349
doi: 10.1038/nrg3980
Gomes T, Teichmann SA, Talavera-López C. Immunology Driven by Large-Scale Single-Cell Sequencing. Trends Immunol. 2019;40:1011–21.
pubmed: 31645299
doi: 10.1016/j.it.2019.09.004
Cheung RK, Utz PJ. CyTOF—the next generation of cell detection. Nat Rev Rheumatol. 2011;7:502–3.
pubmed: 21788983
pmcid: 3387986
doi: 10.1038/nrrheum.2011.110
Spitzer Matthew H, Nolan Garry P. Mass Cytometry: Single Cells. Many Features Cell. 2016;165:780–91.
pubmed: 27153492
Tian Y, Carpp LN, Miller HER, Zager M, Newell EW, Gottardo R. Single-cell immunology of SARS-CoV-2 infection. Nat Biotechnol. 2022;40:30–41.
pubmed: 34931002
doi: 10.1038/s41587-021-01131-y
McKinnon KM: Flow Cytometry: An Overview. Current Protocols in Immunology 2018, 120:5.1.1–5.1.11.
Rao A, Barkley D, França GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature. 2021;596:211–20.
pubmed: 34381231
pmcid: 8475179
doi: 10.1038/s41586-021-03634-9
Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet. 2019;20:631–56.
pubmed: 31341269
doi: 10.1038/s41576-019-0150-2
Ng PC, Kirkness EF. Whole Genome Sequencing. In: Barnes MR, Breen G, editors. Genetic Variation: Methods and Protocols. Totowa, NJ: Humana Press; 2010. p. 215–26.
doi: 10.1007/978-1-60327-367-1_12
Hughes CE, Nibbs RJB. A guide to chemokines and their receptors. Febs j. 2018;285:2944–71.
pubmed: 29637711
pmcid: 6120486
doi: 10.1111/febs.14466
Stadler M, Pudelko K, Biermeier A, Walterskirchen N, Gaigneaux A, Weindorfer C, Harrer N, Klett H, Hengstschläger M, Schüler J, et al. Stromal fibroblasts shape the myeloid phenotype in normal colon and colorectal cancer and induce CD163 and CCL2 expression in macrophages. Cancer Lett. 2021;520:184–200.
pubmed: 34256095
doi: 10.1016/j.canlet.2021.07.006
Davidson S, Coles M, Thomas T, Kollias G, Ludewig B, Turley S, Brenner M, Buckley CD. Fibroblasts as immune regulators in infection, inflammation and cancer. Nat Rev Immunol. 2021;21:704–17.
pubmed: 33911232
doi: 10.1038/s41577-021-00540-z
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573-3587.e3529.
pubmed: 34062119
pmcid: 8238499
doi: 10.1016/j.cell.2021.04.048
Han X, Zhou Z, Fei L, Sun H, Wang R, Chen Y, Chen H, Wang J, Tang H, Ge W, et al. Construction of a human cell landscape at single-cell level. Nature. 2020;581:303–9.
pubmed: 32214235
doi: 10.1038/s41586-020-2157-4
Kariminekoo S, Movassaghpour A, Rahimzadeh A, Talebi M, Shamsasenjan K, Akbarzadeh A. Implications of mesenchymal stem cells in regenerative medicine. Artificial Cells, Nanomedicine, and Biotechnology. 2016;44:749–57.
pubmed: 26757594
doi: 10.3109/21691401.2015.1129620
Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J, et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017;14:1083–6.
pubmed: 28991892
pmcid: 5937676
doi: 10.1038/nmeth.4463
Cillo AR, Kürten CHL, Tabib T, Qi Z, Onkar S, Wang T, Liu A, Duvvuri U, Kim S, Soose RJ, et al. Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer. Immunity. 2020;52:183-199.e189.
pubmed: 31924475
pmcid: 7201194
doi: 10.1016/j.immuni.2019.11.014
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47–e47.
pubmed: 25605792
pmcid: 4402510
doi: 10.1093/nar/gkv007
Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545-d551.
pubmed: 33125081
doi: 10.1093/nar/gkaa970
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.
pubmed: 10802651
pmcid: 3037419
doi: 10.1038/75556
The Gene Ontology resource. enriching a GOld mine. Nucleic Acids Res. 2021;49:D325-d334.
doi: 10.1093/nar/gkaa1113
Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc: Ser B (Methodol). 1995;57:289–300.
doi: 10.1111/j.2517-6161.1995.tb02031.x
Staley JR, Blackshaw J, Kamat MA, Ellis S, Surendran P, Sun BB, Paul DS, Freitag D, Burgess S, Danesh J, et al. PhenoScanner: a database of human genotype-phenotype associations. Bioinformatics. 2016;32:3207–9.
pubmed: 27318201
pmcid: 5048068
doi: 10.1093/bioinformatics/btw373
Kamat MA, Blackshaw JA, Young R, Surendran P, Burgess S, Danesh J, Butterworth AS, Staley JR. PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. Bioinformatics. 2019;35:4851–3.
pubmed: 31233103
pmcid: 6853652
doi: 10.1093/bioinformatics/btz469
Ballardini G, Bianchi F, Doniach D, Mirakian R, Pisi E, Bottazzo G. ABERRANT EXPRESSION OF HLA-DR ANTIGENS ON BILEDUCT EPITHELIUM IN PRIMARY BILIARY CIRRHOSIS: RELEVANCE TO PATHOGENESIS. The Lancet. 1984;324:1009–13.
doi: 10.1016/S0140-6736(84)91108-5
Hirschfield GM, Liu X, Xu C, Lu Y, Xie G, Lu Y, Gu X, Walker EJ, Jing K, Juran BD, et al. Primary Biliary Cirrhosis Associated with HLA, IL12A, and IL12RB2 Variants. N Engl J Med. 2009;360:2544–55.
pubmed: 19458352
pmcid: 2857316
doi: 10.1056/NEJMoa0810440
Peng A, Ke P, Zhao R, Lu X, Zhang C, Huang X, Tian G, Huang J, Wang J, Invernizzi P, et al. Elevated circulating CD14(low)CD16(+) monocyte subset in primary biliary cirrhosis correlates with liver injury and promotes Th1 polarization. Clin Exp Med. 2016;16:511–21.
pubmed: 26403460
doi: 10.1007/s10238-015-0381-2
Chen Y-Y, Arndtz K, Webb G, Corrigan M, Akiror S, Liaskou E, Woodward P, Adams DH, Weston CJ, Hirschfield GM. Intrahepatic macrophage populations in the pathophysiology of primary sclerosing cholangitis. JHEP Reports. 2019;1:369–76.
pubmed: 32039388
pmcid: 7005651
doi: 10.1016/j.jhepr.2019.10.003
Olmos JM, García JD, Jiménez A, de Castro S. Impaired monocyte function in primary biliary cirrhosis. Allergol Immunopathol (Madr). 1988;16:353–8.
pubmed: 3228054
Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J Immunol. 2014;192:2689–98.
pubmed: 24510963
doi: 10.4049/jimmunol.1302064
Borcherding N, Bormann NL, Kraus G. scRepertoire: An R-based toolkit for single-cell immune receptor analysis. F1000Research. 2020;9.
Larbi A, Fulop T. From “truly naïve” to “exhausted senescent” T cells: When markers predict functionality. Cytometry A. 2014;85:25–35.
pubmed: 24124072
doi: 10.1002/cyto.a.22351
Lee S-W, Choi HY, Lee G-W, Kim T, Cho H-J, Oh I-J, Song SY, Yang DH, Cho J-H. CD8<sup>+</sup> TILs in NSCLC differentiate into TEMRA via a bifurcated trajectory: deciphering immunogenicity of tumor antigens. J Immunother Cancer. 2021;9: e002709.
pubmed: 34593620
pmcid: 8487216
doi: 10.1136/jitc-2021-002709
Chen K, Kolls JK. T Cell-Mediated Host Immune Defenses in the Lung. Annu Rev Immunol. 2013;31:605–33.
pubmed: 23516986
pmcid: 3912562
doi: 10.1146/annurev-immunol-032712-100019
Mowat AM, Agace WW. Regional specialization within the intestinal immune system. Nat Rev Immunol. 2014;14:667–85.
pubmed: 25234148
doi: 10.1038/nri3738
Godfrey DI, Koay H-F, McCluskey J, Gherardin NA. The biology and functional importance of MAIT cells. Nat Immunol. 2019;20:1110–28.
pubmed: 31406380
doi: 10.1038/s41590-019-0444-8
Nel I, Bertrand L, Toubal A, Lehuen A. MAIT cells, guardians of skin and mucosa? Mucosal Immunol. 2021;14:803–14.
pubmed: 33753874
pmcid: 7983967
doi: 10.1038/s41385-021-00391-w
Legoux F, Salou M, Lantz O. MAIT Cell Development and Functions: the Microbial Connection. Immunity. 2020;53:710–23.
pubmed: 33053329
doi: 10.1016/j.immuni.2020.09.009
van den Broek T, Borghans JAM, van Wijk F. The full spectrum of human naive T cells. Nat Rev Immunol. 2018;18:363–73.
pubmed: 29520044
doi: 10.1038/s41577-018-0001-y
Soundararajan M, Kannan S. Fibroblasts and mesenchymal stem cells: Two sides of the same coin? J Cell Physiol. 2018;233:9099–109.
pubmed: 29943820
doi: 10.1002/jcp.26860
Muzlifah AH, Matthew PC, Christopher DB, Francesco D. Mesenchymal stem cells: the fibroblasts’ new clothes? Haematologica. 2009;94:258–63.
doi: 10.3324/haematol.13699
Lendahl U, Muhl L, Betsholtz C. Identification, discrimination and heterogeneity of fibroblasts. Nat Commun. 2022;13:3409.
pubmed: 35701396
pmcid: 9192344
doi: 10.1038/s41467-022-30633-9
Steens J, Unger K, Klar L, Neureiter A, Wieber K, Hess J, Jakob HG, Klump H, Klein D. Direct conversion of human fibroblasts into therapeutically active vascular wall-typical mesenchymal stem cells. Cell Mol Life Sci. 2020;77:3401–22.
pubmed: 31712992
doi: 10.1007/s00018-019-03358-0
Ichim TE, O’Heeron P, Kesari S. Fibroblasts as a practical alternative to mesenchymal stem cells. J Transl Med. 2018;16:212.
pubmed: 30053821
pmcid: 6064181
doi: 10.1186/s12967-018-1536-1
Beumer J, Clevers H. Cell fate specification and differentiation in the adult mammalian intestine. Nat Rev Mol Cell Biol. 2021;22:39–53.
pubmed: 32958874
doi: 10.1038/s41580-020-0278-0
Moor AE, Harnik Y, Ben-Moshe S, Massasa EE, Rozenberg M, Eilam R, Bahar Halpern K, Itzkovitz S. Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis. Cell. 2018;175:1156-1167.e1115.
pubmed: 30270040
doi: 10.1016/j.cell.2018.08.063
Kendall RT, Feghali-Bostwick CA. Fibroblasts in fibrosis: novel roles and mediators. Front Pharmacol. 2014;5:123.
pubmed: 24904424
pmcid: 4034148
doi: 10.3389/fphar.2014.00123
Oliver JR, Kushwah R, Wu J, Pan J, Cutz E, Yeger H, Waddell TK, Hu J. Elf3 plays a role in regulating bronchiolar epithelial repair kinetics following Clara cell-specific injury. Lab Invest. 2011;91:1514–29.
pubmed: 21709667
doi: 10.1038/labinvest.2011.100
Ng AYN, Waring P, Ristevski S, Wang C, Wilson T, Pritchard M, Hertzog P, Kola I. Inactivation of the transcription factor Elf3 in mice results in dysmorphogenesis and altered differentiation of intestinal epithelium. Gastroenterology. 2002;122:1455–66.
pubmed: 11984530
doi: 10.1053/gast.2002.32990
Chen R, Kang R, Tang D. The mechanism of HMGB1 secretion and release. Exp Mol Med. 2022;54:91–102.
pubmed: 35217834
pmcid: 8894452
doi: 10.1038/s12276-022-00736-w
Dai S, Sodhi C, Cetin S, Richardson W, Branca M, Neal MD, Prindle T, Ma C, Shapiro RA, Li B, et al. Extracellular High Mobility Group Box-1 (HMGB1) Inhibits Enterocyte Migration via Activation of Toll-like Receptor-4 and Increased Cell-Matrix Adhesiveness 2<sup></sup>. J Biol Chem. 2010;285:4995–5002.
pubmed: 20007974
doi: 10.1074/jbc.M109.067454
Klepsch V, Gerner RR, Klepsch S, Olson WJ, Tilg H, Moschen AR, Baier G, Hermann-Kleiter N. Nuclear orphan receptor NR2F6 as a safeguard against experimental murine colitis. Gut. 2018;67:1434–44.
pubmed: 28779026
doi: 10.1136/gutjnl-2016-313466
Klepsch V, Hermann-Kleiter N, Baier G. Beyond CTLA-4 and PD-1: Orphan nuclear receptor NR2F6 as T cell signaling switch and emerging target in cancer immunotherapy. Immunol Lett. 2016;178:31–6.
pubmed: 26992368
doi: 10.1016/j.imlet.2016.03.007
Sanz-Pamplona R, Berenguer A, Cordero D, Molleví DG, Crous-Bou M, Sole X, Paré-Brunet L, Guino E, Salazar R, Santos C, et al. Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. Mol Cancer. 2014;13:46.
pubmed: 24597571
pmcid: 4023701
doi: 10.1186/1476-4598-13-46
McPherson JP, Sarras H, Lemmers B, Tamblyn L, Migon E, Matysiak-Zablocki E, Hakem A, Azami SA, Cardoso R, Fish J, et al. Essential role for Bclaf1 in lung development and immune system function. Cell Death Differ. 2009;16:331–9.
pubmed: 19008920
doi: 10.1038/cdd.2008.167
Aw S. Sun H, Geng Y, Peng Q, Wang P, Chen J, Xiong T, Cao R, Tang J: Bclaf1 is an important NF-κB signaling transducer and C/EBPβ regulator in DNA damage-induced senescence. Cell Death Differ. 2016;23:865–75.
doi: 10.1038/cdd.2015.150
Zhou X, Li X, Cheng Y, Wu W, Xie Z, Xi Q, Han J, Wu G, Fang J, Feng Y. BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells. Nat Commun. 2014;5:4581.
pubmed: 25091051
doi: 10.1038/ncomms5581
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102:15545–50.
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102
Liberzon A, Subramanian A, Pinchback R. Thorvaldsdottir H, Tamayo P, Mesirov JP: Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27:1739–40.
pubmed: 21546393
pmcid: 3106198
doi: 10.1093/bioinformatics/btr260
GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020;369:1318–30.
doi: 10.1126/science.aaz1776
Pan L, Parini P, Tremmel R, Loscalzo J, Lauschke VM, Maron BA, Paci P, Ernberg I, Tan NS, Liao Z, Yin W, Rengarajan S, Li X: Single Cell Atlas: a single-cell multi-omics human cell encyclopedia. Github. https://github.com/eudoraleer/sca/ ; 2024.
Pan L, Parini P, Tremmel R, Loscalzo J, Lauschke VM, Maron BA, Paci P, Ernberg I, Tan NS, Liao Z, Yin W, Rengarajan S, Wang ZN, Li X: Single Cell Atlas: a single-cell multi-omics human cell encyclopedia. Zenodo. https://zenodo.org/doi/10.5281/zenodo.10906053 ; 2024.