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#DatabaseYearPMIDCitationsURLWeb InterferanceNumber of studies
/dataset		Number of donors
/samples		Number of cellsData sourceCancer types
/Diseases		Number of tissuesNumber of organsSpecific focusSpecific typeDownload availableData Type NormalizationData Type AvailableDownlable Data FormatsData Location Data DownloadGene Expression ExplorationPseudotime patternCell-cell communicationTF activity assessmentsAnnodate your dataCell Type Marker Plot
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1White Adipose Atlas202235296864297https://gitlab.com/rosen-lab/white-adipose-atlasAvailable1928465Primary1Tissue-specificWhite Adipose TissueAvailableSCTransformraw counts + normalizedRDShttps://gitlab.com/rosen-lab/white-adipose-atlasAvailable
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2Vasculature of Adult Brain202235084939136https://cells.ucsc.edu/?ds=adult-brain-vascAvailable15161336Primary1Tissue-specificVascultatureAvailableSCTransform raw counts + normalizedRDShttps://cells.ucsc.edu/?ds=adult-brain-vascAvailable
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3Human Tonsil Atlas20243830165317https://bioconductor.org/packages/release/data/experiment/html/HCATonsilData.htmlNot available117556,000Primary1Tissue-specificTonsilAvailablelog-normalisedraw counts + normalizedRDShttps://zenodo.org/records/8373756Available
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4Human Lung Cell Atlas2020332089461096https://hlca.ds.czbiohub.org/Available1375000Primary1Tissue-specificLungAvailablelog-normalisedraw countsRobjhttps://www.synapse.org/#!Synapse:syn21041850/discussion/defaultAvailable
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5Liver Cell Atlas202031292543785http://human-liver-cell-atlas.ie-freiburg.mpg.de/Available1910000Primary1Tissue-specificLiver Not availableAvailable
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6Liver Cell Atlas202235021063374https://www.livercellatlas.org/datasets_HCA.phpAvailable15167598Primary1Tissue-specificLiverAvailablelog-normalisedraw countsmtxhttps://www.livercellatlas.org/download.phpAvailableAvailable
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7Kidney Cell Atlas201931604275315https://www.kidneycellatlas.org/Available12040268Primary1Tissue-specificKidneyAvailableseurat normaliseraw countsH5ADhttps://www.kidneycellatlas.org/AvailableAvailable
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8Heart Cell Atlas202032971526974https://www.heartcellatlas.org/Available114704296Primary1Tissue-specificHeartAvailablelog-normalisedraw counts + normalizedH5ADhttps://www.heartcellatlas.org/AvailableAvailable
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9CorneaCellAtlas202133865984104http://retinalstemcellresearch.co.uk/CorneaCellAtlas/Available1421343Primary1Tissue-specificCorneaAvailablelog-normalisedraw countsmtxhttp://retinalstemcellresearch.co.uk/CorneaCellAtlas/AvailableAvailable
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10Human Breast Cell Atlas20233738076733https://navinlabcode.github.io/HumanBreastCellAtlas.github.io/Available1126714331Primary1Tissue-specificBreastAvailablelog-normalisedraw countsRDShttps://cellxgene.cziscience.com/collections/4195ab4c-20bd-4cd3-8b3d-65601277e731AvailableAvailable
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11Organoid201931619793547https://bioinf.eva.mpg.de/shiny/sample-apps/scApeX/Available143498Primary1Tissue-specificBrainNot availableAvailableAvailable
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12First-trimester Developing Human Brain20233782465030https://hdca-sweden.scilifelab.se/tissues-overview/brain/Available1261665937Primary1Tissue-specificBrainNot availableAvailable
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13HCA Bone Marrow201830243574179https://www.altanalyze.org/ICGS/HCA/splash.phpAvailable18100000Primary1Tissue-specificBone MarrowAvailablelog-normalisednormalizedxlsxhttps://www.altanalyze.org/ICGS/HCA/Viewer.phpAvailableAvailable
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14Human Cell Landscape202032214235750https://bis.zju.edu.cn/HCL/Available163700,000Primary50GeneralGeneralAvailablelog-normalisedraw countsmtx
H5AD		https://figshare.com/articles/dataset/HCL_DGE_Data/7235471Available
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15Descartes 202133184181486https://descartes.brotmanbaty.org/Available1154000000Primary12115GeneralGeneralAvailableraw counts + normalizedRDShttps://descartes.brotmanbaty.org/bbi/human-gene-expression-during-development/AvailableAvailable
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16Tabula Sapiens202235549404417https://tabula-sapiens-portal.ds.czbiohub.org/Available115500,000Primary24GeneralGeneralAvailableraw counts + normalizedRDShttps://cellxgene.cziscience.com/e/53d208b0-2cfd-4366-9866-c3c6114081bc.cxg/AvailableAvailableAvailable
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17GTEXsinglecellatlas202235549429201https://www.gtexportal.org/home/singleCellOverviewPageAvailable116209126Primary8GeneralGeneralAvailablelog-normalisedraw countsH5ADhttps://www.gtexportal.org/home/downloads/adult-gtex/single_cell Available
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18Kidney Single-Cell Atlas202032978267121http://www.ruuo-kidney-gene-atlas.com/Available1417136Primary1DiseaseKidney DiseaseNot available
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19Kidney Tissue Atlas202337468583161https://cellxgene.cziscience.com/collections/bcb61471-2a44-4d00-a0af-ff085512674cAvailable193584,843Primary1DiseaseKidney DiseaseAvailableSCTransformraw counts + normalizedRDShttps://cellxgene.cziscience.com/collections/bcb61471-2a44-4d00-a0af-ff085512674cAvailableAvailable
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20Covid19 Cell Atlas202133915569586https://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples#study-summaryAvailable132106792Primary11DiseaseCovid-19Availablelog-normalisedraw countsmtxhttps://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples#study-summaryAvailableAvailable
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21Lung Atlas of Lethal COVID-19202233915568458https://singlecell.broadinstitute.org/single_cell/study/SCP1219/columbia-university-nyp-covid-19-lung-atlasAvailable119116314Primary1DiseaseCovid-19Availablelog-normalisedmtxhttps://singlecell.broadinstitute.org/single_cell/study/SCP1219/columbia-university-nyp-covid-19-lung-atlasAvailableAvailable
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22ddnetbio201931768052636http://adsn.ddnetbio.com/Available1613214Primary1DiseaseAlzheimerAvailablelog-normalisedraw counts + normalizedmtxhttp://adsn.ddnetbio.com/AvailableAvailableAvailable
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23Breast Cancer single-cell Atlas20223536181665https://bcatlas.tigem.it/tigem/dibernardo/AIRC_atlas_32_ccls/?ds=Atlas_32_cclsAvailable13235276Primary11CancerBreast CancerAvailableGF-ICFraw countsmtxhttps://figshare.com/articles/dataset/Single_Cell_Breast_Cancer_cell-line_Atlas/15022698Available
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24Single Cell Breast Cancer2023371586904https://mikaqiao.shinyapps.io/scBC/Available121117958Primary11CancerBreast CancerNot availableAvailable
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25GEO/SRA2013231932588811https://www.ncbi.nlm.nih.gov/geo/Available112585AggregatedGeneralGeneralAvailablemixedmixedmixedhttps://www.ncbi.nlm.nih.gov/geo/Available
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26scRNA-seq package2016NA0https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.htmlNot available611641896AggregatedGeneralGeneralAvailablemixedraw countsR libraryhttps://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.htmlAvailable
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27Human Cell Atlas2017292061041942https://data.humancellatlas.org/Available437860058500000Aggregated18GeneralGeneralAvailablemixedmixedmixedhttps://explore.data.humancellatlas.org/projectsAvailableAvailable
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28scRNASeqDB20172920616791https://bioinfo.uth.edu/scrnaseqdb/Available3813,44013440AggregatedGeneralGeneralNot availableAvailable
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29Single Cell Expression Atlas 201831665515475https://www.ebi.ac.uk/gxa/sc/homeAvailable14710,505,726AggregatedGeneralGeneralAvailablelog-normalisedraw counts + normalizedmtxhttps://www.ebi.ac.uk/gxa/sc/downloadAvailableAvailableAvailable
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30SCPortalen20182904571351http://single-cell.clst.riken.jp/Available2320,761AggregatedGeneralGeneralNot availableAvailable
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31SCDevDB20193161190920https://scdevdb.deepomics.orgAvailable3813,440AggregatedGeneralGeneralNot availableAvailable
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32PanglaoDB201930951143867https://panglaodb.se/Available3051,126,580Aggregated74GeneralGeneralAvailablelog-normalisedraw counts + normalizedRData https://panglaodb.se/bulk.htmlAvailableAvailable
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33HuBMAP201931597973368https://portal.hubmapconsortium.org/Available23621843Aggregated31GeneralGeneralNot availableAvailable
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34Curated Database202033247933174https://docs.google.com/spreadsheets/d/1En7-UV0k0laDiIfjFkdn7dggyR7jIk3WH8QgXaMOZF0/edit#gid=0Not available1946134393568AggregatedGeneralGeneralNot available
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35Human Protein Atlas202134321199749https://www.proteinatlas.org/humanproteome/single+cell+type Available14174271Aggregated1314+GeneralGeneralAvailablepTPMraw countstsvhttps://www.proteinatlas.org/about/downloadAvailableAvailable
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36Single Cell Portal2021375029048https://singlecell.broadinstitute.org/single_cellAvailable65440,699,488AggregatedGeneralGeneralAvailablemixedmixedmixedhttps://singlecell.broadinstitute.org/single_cellAvailableAvailable
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37UCSC Cell Browser202134244710127https://cells.ucsc.edu/?Available378AggregatedGeneralGeneralAvailablemixedmixedmixedhttps://cells.ucsc.edu/?AvailableAvailable
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38gEAR202134172972112https://www.umgear.org/Available1180AggregatedGeneralGeneralNot availableAvailable
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39DISCO20223479137555https://www.immunesinglecell.org/Available1,07713,99861,280,618Aggregated393174GeneralGeneralAvailablelog-normalisedH5AD
RDS		https://www.immunesinglecell.org/downloadAvailableAvailableAvailable
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40singleCellBase2023377306273http://cloud.capitalbiotech.com/SingleCellBase/Available4649,158Aggregated464165GeneralGeneralNot availableAvailable
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41SingleScan2023380623570http://cailab.labshare.cn/SingleScanAvailable1093077622Aggregated495+GeneralGeneralNot availableAvailable
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42AgeAnno20233620083814https://relab.xidian.edu.cn/AgeAnno/#/Available2261,298,996Aggregated2817GeneralGeneralAvailablelog-normalisedraw countsRDShttps://drive.google.com/drive/folders/14fw8OtqRMOZNbMIGhLSaf1G-N9MsdctbAvailableAvailableAvailableAvailableAvailable
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43scBrainMap2023371956962https://scbrainmap.sysneuro.net/Available7156577222Aggregated201GeneralGeneralNot availableAvailableAvailable
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44Human Transcriptome Cell Atlas20233613026614https://www.htcatlas.org/Available1924652615Aggregated19GeneralGeneralAvailableSCTransform raw countsRDShttps://www.htcatlas.org/downloadAvailableAvailableAvailableAvailableAvailable
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45Human Universal Single Cell Hub20233631825810http://husch.comp-genomics.org/#/searchAvailable185300000Aggregated45GeneralGeneralAvailablemtxintegratedH5http://husch.comp-genomics.org/#/infoAvailableAvailableAvailable
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46Cellxgene2023https://doi.org/10.1101/2021.04.05.43831854https://cellxgene.cziscience.com/Available128485100000AggregatedGeneralGeneralAvailablemixedraw counts + normalizedRDShttps://cellxgene.cziscience.com/datasetsAvailableAvailable
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47SCInter2023381252970https://bio.liclab.net/SCInter/index.phpAvailable1151016AggregatedGeneralGeneralNot availableAvailableAvailable
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48OrganoidDB2023362717924http://www.inbirg.com/organoid_db/Available145670000Aggregated141GeneralGeneralNot availableAvailable
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49SC2sepsis2022359802861http://www.rjh-sc2sepsis.com/indexAvailable71232226Aggregated1DiseaseSepsisNot availableAvailable
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50SC2disease20213301017767http://easybioai.com/sc2disease/Available946481Aggregated2529DiseaseMultipleNot availableAvailable
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51Human Lung Cell Atlas202337291214130https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293Available494862,400,000Aggregated154DiseaseLung DiseaseAvailablelog-normalisedraw counts + normalizedRDShttps://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293AvailableAvailable
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52Covid19cellatlas2020323277582678https://www.covid19cellatlas.org/Available15Aggregated129DiseaseCovid-19Availablelog-normalizedraw countsH5ADhttps://www.covid19cellatlas.org/meyer21_airway/AvailableAvailable
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53SCovid20223463482030http://bio-annotation.cn/scovidNot available211042227Aggregated110DiseaseCovid-19AvailableSCTransform raw countstxthttp://bio-computing.hrbmu.edu.cn/scovid/#/downloadAvailableAvailableAvailable
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54scREAD20203324120574https://bmbls.bmi.osumc.edu/scread/ Available73713,640Aggregated1DiseaseAlzheimerAvailableraw countsRDShttps://bmbls.bmi.osumc.edu/scread/downloadsAvailableAvailableAvailable
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55ssREAD2023377455920https://bmblx.bmi.osumc.edu/ssread/Available352,572,355Aggregated1DiseaseAlzheimerNot available
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56SCAD-Brain2023372518044https://www.bioinform.cn/SCAD/Available213591,564,825Aggregated110DiseaseAlzheimerNot availableAvailableAvailableAvailable
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57JingleBells2017284167140https://jinglebells.bgu.ac.il/Available302AggregatedCell typeImmune CellsNot available
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58EndoDB20193035737978https://endotheliomics.shinyapps.io/endodb/Available3605847Aggregated15+Cell typeEndothelial CellsAvailablehttps://endotheliomics.shinyapps.io/endodb/AvailableAvailable
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59huARdb2022346066169https://huarc.net/v2/Available215444794Aggregated1224Cell typeImmune CellsNot available
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60ABC portal2023359203309http://abc.sklehabc.com/#/homeAvailable1983878881Aggregated5910+Cell typeBlood CellsAvailablelog-normalizedraw countsRDShttp://abc.sklehabc.com/#/searchAvailableAvailableAvailable
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61CancerSEA201930329142505http://biocc.hrbmu.edu.cn/CancerSEA/Available7493,475Aggregated27CancerMultipleNot availableAvailable
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62scTIME20213411708533http://scTIME.sklehabc.comAvailable49196273Aggregated39CancerMultipleNot availableAvailable
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63TISCH202133179754542http://tisch1.comp-genomics.org/Available762,045,746Aggregated27CancerMultipleAvailablelog-normalizednormalizedmtxhttp://tisch1.comp-genomics.org/gallery/AvailableAvailableAvailableAvailable
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64Compendium papers1202134914499485http://cancer-pku.cn:3838/PanC_T/Available37316397,810Aggregated21CancerMultipleNot availableAvailable
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65Tumor Immune Cell Atlas20213454832399https://singlecellgenomics-cnag-crg.shinyapps.io/TICA/Available16217500,000Aggregated13CancerMultipleAvailablelog-normalizedintegratedH5AD
RDS		https://zenodo.org/records/5205544AvailableAvailableAvailable
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66TMExplorer2022360840819https://figshare.com/projects/TMExplorer_A_Tumour_Microenvironment_Single-cell_RNAseq_Database_and_Search_Tool/101471Available481438299Aggregated26CancerMultipleAvailablemixedmixedRDShttps://figshare.com/projects/TMExplorer_A_Tumour_Microenvironment_Single-cell_RNAseq_Database_and_Search_Tool/101471Available
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67cancerSCEM20223464372552https://ngdc.cncb.ac.cn/cancerscemAvailable28638,341Aggregated20CancerMultipleAvailablelog-normalizedraw countstsvhttps://ngdc.cncb.ac.cn/cancerscem/downloadsAvailableAvailableAvailable
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68Compendium papers2202236333338129https://gist-fgl.github.io/sc-caf-atlas/Available12226855,271Aggregated1010CancerMultipleNot available
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69IMMUcanDB20233645956412https://immucanscdb.vital-it.ch/Available1444474385Aggregated56CancerMultipleAvailablelog-normalizedH5ADhttps://immucanscdb.vital-it.ch/AvailableAvailableAvailable
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70TISCH220233632166282http://tisch.comp-genomics.org/Available1906,297,320Aggregated50CancerMultipleAvailablelog-normalizednormalizedmtxhttp://tisch.comp-genomics.org/AvailableAvailableAvailableAvailable
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71Curated Cancer Atlas20233725868251https://www.weizmann.ac.il/sites/3CA/Available772,591,545Aggregated24CancerMultipleAvailableTPMraw counts/TPMmtxhttps://www.weizmann.ac.il/sites/3CA/AvailableAvailable
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72Pan-cancer T cell atlas20233724830154https://singlecell.mdanderson.org/ Available27670656,742Aggregated1621CancerMultipleNot availableAvailableAvailable
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73SCAR2024377394052http://8.142.154.29/SCAR2023/Available19011301352Aggregated21395CancerMultipleNot available
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74scRNA-seq-ICB-cohorts2024383281530https://zenodo.org/records/10407126Available890270Aggregated9CancerMultipleAvailablelog-normalisedraw countsRDShttps://zenodo.org/records/10407126AvailableAvailable
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