This package provides functions for retrieving SingleCellExperiment representations of data from 55 single-cell RNA-seq experiments.
Functions to call after running library(scRNAseq) are
listed in the 'call' column of the table:
| org | part | title | count | pmid | call |
| Xenopus laevis | tail | Identification of a regeneration-organizing cell in the Xenopus tail | 13199 | 31097661 | AztekinTailData() |
| Mus musculus | mammary gland | Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing | 25806 | 29225342 | BachMammaryData() |
| Homo sapiens | T cells | Low-Avidity CD4+ T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19 | 104417 | 33296686 | BacherTCellData() |
| Homo sapiens | pancreas | A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure | 8569 | 27667365 | BaronPancreasData('human') |
| Mus musculus | pancreas | A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure | 1886 | 27667365 | BaronPancreasData('mouse') |
| Homo sapiens | cortical organoids | Cell stress in cortical organoids impairs molecular subtype specification | 242349 | 31996853 | BhaduriOrganoidData() |
| Mus musculus | embryonic stem cells | Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells | 288 | 25599176 | BuettnerESCData() |
| Homo sapiens | haematopoietic stem and progenitor | Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells | 5183 | 33406429 | BunisHSPCData() |
| Mus musculus | brain | A molecular census of arcuate hypothalamus and median eminence cell types | 21086 | 28166221 | CampbellBrainData() |
| Mus musculus | brain | Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity | 14437 | 28355573 | ChenBrainData() |
| Homo sapiens | brain | A survey of human brain transcriptome diversity at the single cell level | 466 | 26060301 | DarmanisBrainData() |
| Mus musculus | testis | Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis | 68937 | 30890697 | ErnstSpermatogenesisData() |
| Mus musculus | olfactory epithelium | Deconstructing olfactory stem cell trajectories at single-cell resolution | 616 | 28506465 | FletcherOlfactoryData() |
| Mus musculus | haematopoietic stem cells | De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data | 1915 | 27345837 | GrunHSCData() |
| Homo sapiens | pancreas | De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data | 1728 | 27345837 | GrunPancreasData() |
| Mus musculus | haematopoietic stem cells | Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis | 81024 | 29915358 | GiladiHSCData(mode='rna') |
| Homo sapiens | various organs | Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs | 84363 | 33287869 | HeOrganAtlasData() |
| Mus musculus | spermatogenic cells | The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids | 2325 | 30404016 | HermannSpermatogenesisData() |
| Mus musculus | cortex | Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-seq | 48000 | 29220646 | HuCortexData() |
| Mus musculus | embryonic stem cells | Single cell RNA-Sequencing of pluripotent states unlocks modular transcriptional variation | 704 | 26431182 | KolodziejczykESCData() |
| Mus musculus | brain | Stalled developmental programs at the root of pediatric brain tumors | 61595 | 31768071 | JessaBrainData() |
| Homo sapiens | embryonic stem cells | Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells | 1715 | 25420068 | LaMannoBrainData('human-es') |
| Homo sapiens | embryonic midbrain | Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells | 1977 | 25420068 | LaMannoBrainData('human-embryo') |
| Homo sapiens | induced pluripotent stem cells | Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells | 337 | 25420068 | LaMannoBrainData('human-ips') |
| Mus musculus | adult dopaminergic neurons | Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells | 243 | 25420068 | LaMannoBrainData('mouse-adult') |
| Homo sapiens | embyronic midbrain | Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells | 1907 | 25420068 | LaMannoBrainData('mouse-embryo') |
| Homo sapiens | pancreas | Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes | 638 | 27864352 | LawlorPancreasData() |
| Homo sapiens | bone marrow plasma cells | Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma | 51840 | 30523328 | LedergorMyelomaData() |
| Homo sapiens | embryonic stem cells | Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments | 460 | 26301841 | LengESCData() |
| Mus musculus | 416B cells | Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data | 192 | 29030468 | LunSpikeInData('416b') |
| Mus musculus | trophoblasts | Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data | 192 | 29030468 | LunSpikeInData('tropho') |
| Mus musculus | retina | Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets | 49300 | 26000488 | MacoskoRetinaData() |
| Mus musculus | T helper cells | Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis | 96 | 24813893 | ReprocessedTh2Data() |
| Homo sapiens | peripheral blood mononuclear cells | A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level | 29033 | 32268080 | MairPBMCData() |
| Homo sapiens | peripheral blood mononuclear cells | Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus | 58654 | 32094927 | KotliarovPBMCData() |
| Mus musculus | brain | Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system | 5069 | 27284195 | MarquesBrainData() |
| Homo sapiens | embryonic stem cells | Transcriptional heterogeneity in naive and primed human pluripotent stem cells at single-cell resolution | 1344 | 30673604 | MessmerESCData() |
| Homo sapiens | pancreas | A Single-Cell Transcriptome Atlas of the Human Pancreas | 3072 | 27693023 | MuraroPancreasData() |
| Mus musculus | haematopoietic stem cells | A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation | 1920 | 27365425 | NestorowaHSCData() |
| Homo sapiens | cortex | Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex | 4261 | 29217575 | NowakowskiCortexData() |
| Mus musculus | haematopoietic stem cells | Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors | 10368 | 26627738 | PaulHSCData() |
| Homo sapiens | cortex | Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex | 65 | 25086649 | ReprocessedFluidigmData() |
| Homo sapiens | outer radial glia | Molecular identity of human outer radial glia during cortical development | 367 | 26406371 | PollenGliaData() |
| Mus musculus | CD8+ T cells | T cell cytolytic capacity is independent of initial stimulation strength | 572 | 30013148 | RichardTCellData() |
| Mus musculus | brain | Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes | 2881 | 27991900 | RomanovBrainData() |
| Homo sapiens | pancreas | Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes | 3514 | 27667667 | SegerstolpePancreasData() |
| Mus musculus | retina | Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics | 44994 | 27565351 | ShekharRetinaData() |
| Mus musculus | peripheral blood mononuclear cells | Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | 50000 | 30567574 | StoeckiusHashingData(mode='mouse') |
| Homo sapiens | peripheral blood mononuclear cells | Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | 50000 | 30567574 | StoeckiusHashingData(mode='human') |
| Homo sapiens | HEK, THP1, K562, KG1 cells | Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | 30000 | 30567574 | StoeckiusHashingData(type='mixed') |
| Mus musculus | brain | Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing | 864 | 25420068 | UsoskinBrainData() |
| Mus musculus | brain | Adult mouse cortical cell taxonomy revealed by single cell transcriptomics | 1809 | 26727548 | TasicBrainData() |
| Mus musculus | visual cortex | Adult mouse cortical cell taxonomy revealed by single cell transcriptomics | 379 | 26727548 | ReprocessedAllenData() |
| Mus musculus | kidney | Advantages of single-nucleus over single-cell RNA sequencing of adult kidney: rare cell types and novel cell states revealed in fibrosis | 17542 | 30510133 | WuKidneyData() |
| Homo sapiens | pancreas | RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes | 1600 | 27667665 | XinPancreasData() |
| Mus musculus | brain | Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq | 3005 | 25700174 | ZeiselBrainData() |
| Mus musculus | nervous system | Molecular Architecture of the Mouse Nervous System | 160796 | 30096314 | ZeiselNervousData() |
| Homo sapiens | liver immune cells | Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human | 68100 | 32351704 | ZhaoImmuneLiverData() |
| Homo sapiens | prefrontal cortex | A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex | 2394 | 29539641 | ZhongPrefrontalData() |
| Homo sapiens | lung | Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species | 173954 | 30979687 | ZilionisLungData() |
| Mus musculus | lung | Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species | 17549 | 30979687 | ZilionisLungData('mouse') |
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