├── .BBSoptions ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── AztekinTailData.R ├── BachMammaryData.R ├── BacherTCellData.R ├── BaronPancreasData.R ├── BhaduriOrganoidData.R ├── BuettnerESCData.R ├── BunisHSPCData.R ├── CampbellBrainData.R ├── ChenBrainData.R ├── DarmanisBrainData.R ├── ERCCSpikeInConcentrations.R ├── ErnstSpermatogenesisData.R ├── FletcherOlfactoryData.R ├── GiladiHSCData.R ├── GrunHSCData.R ├── GrunPancreasData.R ├── HeOrganAtlasData.R ├── HermannSpermatogenesisData.R ├── HuCortexData.R ├── JessaBrainData.R ├── KolodziejczykESCData.R ├── KotliarovPBMCData.R ├── LaMannoBrainData.R ├── LawlorPancreasData.R ├── LedergorMyelomaData.R ├── LengESCData.R ├── LunSpikeInData.R ├── MacoskoRetinaData.R ├── MairPBMCData.R ├── MarquesBrainData.R ├── MessmerESCData.R ├── MuraroPancreasData.R ├── NestorowaHSCData.R ├── NowakowskiCortexData.R ├── PaulHSCData.R ├── PollenGliaData.R ├── ReprocessedData.R ├── RichardTCellData.R ├── RomanovBrainData.R ├── SegerstolpePancreasData.R ├── ShekharRetinaData.R ├── StoeckiusHashingData.R ├── TasicBrainData.R ├── UsoskinBrainData.R ├── WuKidneyData.R ├── XinPancreasData.R ├── ZeiselBrainData.R ├── ZeiselNervousData.R ├── ZhaoImmuneLiverData.R ├── ZhongPrefrontalData.R ├── ZilionisLungData.R ├── convert_to_ensembl.R ├── countErccMolecules.R ├── create_sce.R ├── fetchDataset.R ├── listDatasets.R ├── listPaths.R ├── listVersions.R ├── polishDataset.R ├── saveDataset.R ├── searchDatasets.R └── surveyDatasets.R ├── README.md ├── inst ├── NEWS.Rd └── extdata │ ├── 2.0.0 │ ├── metadata-aztekin-tail.csv │ ├── metadata-bach-mammary.csv │ ├── metadata-baron-pancreas.csv │ ├── metadata-buettner-esc.csv │ ├── metadata-campbell-brain.csv │ ├── metadata-chen-brain.csv │ ├── metadata-grun-hsc.csv │ ├── metadata-grun-pancreas.csv │ ├── metadata-kolodziejczyk-esc.csv │ ├── metadata-lamanno-brain.csv │ ├── metadata-lawlor-pancreas.csv │ ├── metadata-legacy.csv │ ├── metadata-leng-esc.csv │ ├── metadata-lun-spikein.csv │ ├── metadata-macosko-retina.csv │ ├── metadata-marques-brain.csv │ ├── metadata-messmer-esc.csv │ ├── metadata-muraro-pancreas.csv │ ├── metadata-nestorowa-hsc.csv │ ├── metadata-richard-tcell.csv │ ├── metadata-romanov-brain.csv │ ├── metadata-segerstolpe-pancreas.csv │ ├── metadata-shekhar-retina.csv │ ├── metadata-tasic-brain.csv │ ├── metadata-usoskin-brain.csv │ ├── metadata-xin-pancreas.csv │ └── metadata-zeisel-brain.csv │ ├── 2.2.0 │ ├── metadata-ercc-concentrations.csv │ └── metadata-paul-hsc.csv │ ├── 2.4.0 │ ├── metadata-hermann-spermatogenesis.csv │ ├── metadata-hu-cortex.csv │ ├── metadata-kotliarov-pbmc.csv │ ├── metadata-mair-pbmc.csv │ ├── metadata-stoeckius-hashing.csv │ ├── metadata-wu-kidney.csv │ └── metadata-zilionis-lung.csv │ ├── 2.6.0 │ ├── metadata-bacher-tcell.csv │ ├── metadata-bhaduri-organoid.csv │ ├── metadata-bunis-hspc.csv │ ├── metadata-darmanis-brain.csv │ ├── metadata-ernst-spermatogenesis.csv │ ├── metadata-fletcher-olfactory.csv │ ├── metadata-giladi-hsc.csv │ ├── metadata-he-organ-atlas.csv │ ├── metadata-jessa-brain.csv │ ├── metadata-nowakowski-cortex.csv │ ├── metadata-pollen-glia.csv │ ├── metadata-zeisel-nervous.csv │ ├── metadata-zhao-immune-liver.csv │ └── metadata-zhong-prefrontal.csv │ ├── 2.8.0 │ └── metadata-ledergor-myeloma.csv │ └── manifest.csv ├── longtests ├── testthat.R └── testthat │ ├── test-bacher-tcell.R │ ├── test-bhaduri-organoid.R │ ├── test-bunis-hspc.R │ ├── test-darmanis-brain.R │ ├── test-ernst-spermatogenesis.R │ ├── test-fletcher-olfactory.R │ ├── test-giladi-hsc.R │ ├── test-he-organ-atlas.R │ ├── test-jessa-brain.R │ ├── test-ledergor-myeloma.R │ ├── test-nowakowski-cortex.R │ ├── test-pollen-glia.R │ ├── test-zeisel-nervous.R │ ├── test-zhao-immune-liver.R │ └── test-zhong-prefrontal.R ├── man ├── AztekinTailData.Rd ├── BachMammaryData.Rd ├── BacherTCellData.Rd ├── BaronPancreasData.Rd ├── BhaduriOrganoidData.Rd ├── BuettnerESCData.Rd ├── BunisHSPCData.Rd ├── CampbellBrainData.Rd ├── ChenBrainData.Rd ├── DarmanisBrainData.Rd ├── ERCCSpikeInConcentrations.Rd ├── ErnstSpermatogenesisData.Rd ├── FletcherOlfactoryData.Rd ├── GiladiHSCData.Rd ├── GrunHSCData.Rd ├── GrunPancreasData.Rd ├── HeOrganAtlasData.Rd ├── HermannSpermatogenesisData.Rd ├── HuCortexData.Rd ├── JessaBrainData.Rd ├── KolodziejczykESCData.Rd ├── KotliarovPBMCData.Rd ├── LaMannoBrainData.Rd ├── LawlorPancreasData.Rd ├── LedergorMyelomaData.Rd ├── LengESCData.Rd ├── LunSpikeInData.Rd ├── MacoskoRetinaData.Rd ├── MairPBMCData.Rd ├── MarquesBrainData.Rd ├── MessmerESCData.Rd ├── MuraroPancreasData.Rd ├── NestorowaHSCData.Rd ├── NowakowskiCortexData.Rd ├── PaulHSCData.Rd ├── PollenGliaData.Rd ├── ReprocessedData.Rd ├── RichardTCellData.Rd ├── RomanovBrainData.Rd ├── SegerstolpePancreasData.Rd ├── ShekharRetinaData.Rd ├── StoeckiusHashingData.Rd ├── TasicBrainData.Rd ├── UsoskinBrainData.Rd ├── WuKidneyData.Rd ├── XinPancreasData.Rd ├── ZeiselBrainData.Rd ├── ZeiselNervousData.Rd ├── ZhaoImmuneLiverData.Rd ├── ZhongPrefrontalData.Rd ├── ZilionisLungData.Rd ├── countErccMolecules.Rd ├── fetchDataset.Rd ├── listDatasets.Rd ├── listPaths.Rd ├── listVersions.Rd ├── polishDataset.Rd ├── reexports.Rd ├── saveDataset.Rd ├── scRNAseq-package.Rd ├── searchDatasets.Rd └── surveyDatasets.Rd ├── scripts ├── .gitignore ├── aztekin-tail-2019 │ └── 2023-12-14.Rmd ├── bach-mammary-2017 │ └── 2023-12-14.Rmd ├── bacher-tcell-2020 │ └── 2023-12-21.Rmd ├── baron-pancreas-2016 │ └── 2023-12-14.Rmd ├── bhaduri-organoid-2020 │ └── 2023-12-21.Rmd ├── buettner-esc-2015 │ ├── 2023-12-14.Rmd │ └── 2024-04-18.Rmd ├── bunis-hspc-2021 │ └── 2023-12-21.Rmd ├── campbell-brain-2017 │ └── 2023-12-14.Rmd ├── cao-pancreas-2025 │ └── 2025-10-10.Rmd ├── chen-brain-2017 │ └── 2023-12-14.Rmd ├── darmanis-brain-2015 │ └── 2023-12-21.Rmd ├── ercc │ └── 2023-12-20.Rmd ├── ernst-spermatogenesis-2019 │ └── 2023-12-21.Rmd ├── fletcher-olfactory-2019 │ └── 2023-12-21.Rmd ├── giladi-hsc-2018 │ └── 2023-12-21.Rmd ├── grun-bone_marrow-2016 │ └── 2023-12-14.Rmd ├── grun-pancreas-2016 │ └── 2023-12-14.Rmd ├── he-organs-2020 │ └── 2023-12-21.Rmd ├── hu-cortex-2017 │ └── 2023-12-20.Rmd ├── jessa-brain-2019 │ └── 2023-12-22.Rmd ├── kolodziejczyk-esc-2015 │ └── 2023-12-17.Rmd ├── kotliarov-pbmc-2020 │ ├── 2023-12-20.Rmd │ └── 2024-04-18.Rmd ├── lamanno-brain-2016 │ └── 2023-12-17.Rmd ├── lawlor-pancreas-2017 │ └── 2023-12-17.Rmd ├── ledergor-myeloma-2018 │ └── 2023-12-20.Rmd ├── legacy │ └── 2023-12-18.Rmd ├── leng-esc-2015 │ ├── 2023-12-18.Rmd │ ├── 2024-04-18.Rmd │ └── 2024-04-25.Rmd ├── lun-spikein-2017 │ └── 2023-12-18.Rmd ├── macosko-retina-2015 │ └── 2023-12-19.Rmd ├── mair-pbmc-2020 │ ├── 2023-12-20.Rmd │ └── 2024-04-18.Rmd ├── marques-brain-2016 │ └── 2023-12-19.Rmd ├── messmer-esc-2019 │ └── 2023-12-19.Rmd ├── muraro-pancreas-2016 │ └── 2023-12-19.Rmd ├── nestorowa-hsc-2016 │ ├── 2023-12-19.Rmd │ └── 2024-04-18.Rmd ├── nowakowski-cortex-2017 │ └── 2023-12-22.Rmd ├── paul-hsc-2015 │ └── 2023-12-20.Rmd ├── pollen-glia-2015 │ └── 2023-12-22.Rmd ├── richard-tcell-2018 │ └── 2023-12-19.Rmd ├── romanov-brain-2017 │ └── 2023-12-19.Rmd ├── segerstolpe-pancreas-2016 │ └── 2023-12-19.Rmd ├── shekhar-retina-2016 │ └── 2023-12-19.Rmd ├── splicing-demonstration-2020 │ ├── 2023-12-20.Rmd │ ├── alignment.Rmd │ └── ref.bib ├── stoeckius-hashing-2018 │ ├── 2023-12-20.Rmd │ └── 2024-04-18.Rmd ├── tasic-brain-2016 │ ├── 2023-12-19.Rmd │ └── 2024-04-18.Rmd ├── usoskin-brain-2015 │ └── 2023-12-19.Rmd ├── wu-kidney-2019 │ └── 2023-12-20.Rmd ├── xin-pancreas-2016 │ └── 2023-12-19.Rmd ├── zeisel-brain-2015 │ └── 2023-12-14.Rmd ├── zeisel-nervous-2018 │ └── 2023-12-22.Rmd ├── zhao-immune-2020 │ └── 2023-12-22.Rmd ├── zhong-prefrontal-2018 │ └── 2023-12-22.Rmd └── zilionis-lung-2019 │ └── 2023-12-20.Rmd ├── tests ├── testthat.R └── testthat │ ├── test-fetchDataset.R │ ├── test-listPaths.R │ ├── test-loading.R │ ├── test-polishDataset.R │ ├── 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