get_ctd: Import precomputed CellTypeDatasets

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Import precomputed CellTypeDatasets

Description

Import CellTypeDatasets (CTD) generated by EWCE.

• "ctd_AIBS"
  CTD file derived from adult human cortex scRNA-seq data collected by the Allen Institute for Brain Science (AIBS) Note that this CTD used an early release of the AIBS data that only included samples from human Medial Temporal Gyrus (MTG).
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-019-1506-7")}
  Allen Brain Institute website
  Source

• "ctd_allAIBS"
  CTD file derived from adult human cortex scRNA-seq data collected by the Allen Institute for Brain Science (AIBS) Note that this CTD used an later release of the AIBS data that included samples from multiple human brain regions.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-019-1506-7")}
  Allen Brain Institute website
  Source

• "ctd_allKI"
  CTD file with cortex, hippocampus, hypothalamus and midbrain.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41588-018-0129-5")}
  Source

• "ctd_BlueLake2018_FrontalCortexOnly"
  CTD file with data from humans.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.4038")}
  Source

• "ctd_BlueLake2018_VisualCortexOnly"
  CTD file with data from humans.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.4038")}
  Source

• "ctd_Saunders"
  CTD file with data from humans.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2018.07.028")}
  Source

• "ctd_DescartesHuman"
  CTD file with scRNA-seq data from human embryo across multiple organ systems.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.aba7721")}
  Source

• "ctd_DRONC_human"
  CTD file with DRONC-seq data from humans.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nmeth.4407")}
  Source

• "ctd_DRONC_mouse"
  CTD file with Tasic data from mouse.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nmeth.4407")}
  Reference

• "ctd_DivSeq"
  CTD file with DivSeq data.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.aad7038")}
  Source

• "ctd_Tasic"
  CTD file with Tasic data.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nn.4216")}
  Source

• "ctd_Zeisel2016"
  CTD file with data from adult mouse hippocampus.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.aaa1934")}
  Source

• "ctd_Zeisel2018"
  CTD file with data from juvenile mouse central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2018.06.021")}
  Source

• "ctd_LaManno2020"
  CTD file with data from developing mouse central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-021-03775-x")}
  Source

• "ctd_Aerts2018"
  CTD file with data from aging fly central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2018.05.057")}
  Source

• "ctd_FlyCellAtlas"
  CTD file with data from adult fly whole-body atlas (a.k.a the FlyCellAtlas).
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1126/science.abk2432")}
  Source

• "ctd_Raj2018"
  CTD file with data from juvenile zebrafish central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.4103")}
  Source

• "ctd_Raj2020"
  CTD file with data from developing zebrafish central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.neuron.2020.09.023")}
  Source

• "ctd_Farnsworth2020"
  CTD file with data from developing zebrafish central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ydbio.2019.11.008")}
  Source

• "ctd_TabulaMuris_facs"
  CTD file with data from adult mouse whole-body atlas. Uses the Smart-seq2 (FACS) subset of the data and covers a greater number of cell-types than the Droplet version.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-018-0590-4")}
  Source

• "ctd_TabulaMuris_droplet"
  CTD file with data from adult mouse whole-body atlas. Uses the Droplet subset of the data
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-018-0590-4")}
  Source

• "ctd_TabulaMurisSenis" (Under construction)
  CTD file with data from aging adult mouse whole-body atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-020-2496-1")}
  Source

• "ctd_Avalos2019"
  CTD file with data from developing fly central nervous system atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.7554/eLife.50354")}
  Source

• "ctd_NonHumanPrimateCellAtlas"
  CTD file with data from adult monkey whole-body atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-022-04587-3")}
  Source

• "ctd_DescartesMouse"
  CTD file with data from the Descartes developing mouse whole-body atlas.
  Reference: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-019-0969-x")}
  Source

Usage

get_ctd(
  ctd_name = c("ctd_AIBS", "ctd_allKI", "ctd_BlueLake2018_FrontalCortexOnly",
    "ctd_BlueLake2018_VisualCortexOnly", "ctd_DivSeq", "ctd_DRONC_human",
    "ctd_DRONC_mouse", "ctd_Saunders", "ctd_Tasic", "ctd_Zeisel2015", "ctd_Zeisel2018",
    "ctd_TabulaMuris_facs", "ctd_TabulaMuris_droplet", "ctd_Aerts2018",
    "ctd_FlyCellAtlas", "ctd_Avalos2019", "ctd_DescartesHuman", "ctd_DescartesMouse",
    "ctd_HumanCellLandscape", "ctd_Jiang2021", "ctd_NonHumanPrimateCellAtlas",
    "ctd_Raj2018", "ctd_Raj2018", "ctd_Farnsworth2020"),
  tag = "v2.0.8",
  .token = gh::gh_token(),
  storage_dir = tools::R_user_dir(package = "MAGMA.Celltyping", which = "cache")
)

Arguments

ctd_name	Name of one or more CellTypeDatset objects to import.
tag	tag for the GitHub release to which this data should be attached.
.token	GitHub authentication token, see ⁠[gh::gh_token()]⁠
storage_dir	Folder in which to save the CellTypeDatset.

Value

CellTypeDataset object, or a named list of CellTypeDataset objects.

Examples

ctd <- MAGMA.Celltyping::get_ctd("ctd_AIBS")

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.