scfetch (version 0.5.0)

ExtractCELLxGENEMeta: Extract Metadata of CELLxGENE Datasets with Attributes.

Description

Extract Metadata of CELLxGENE Datasets with Attributes.

Usage

ExtractCELLxGENEMeta(
  all.samples.df,
  organism = NULL,
  ethnicity = NULL,
  sex = NULL,
  tissue = NULL,
  disease = NULL,
  assay = NULL,
  suspension.type = NULL,
  cell.type = NULL,
  cell.num = NULL
)

Value

Dataframe contains filtered datasets.

Arguments

all.samples.df

All detail information of CELLxGENE datasets, obtained with ShowCELLxGENEDatasets.

organism

The organism of the datasets, choose from "Homo sapiens", "Mus musculus", "Callithrix jacchus", "Macaca mulatta", "Sus scrofa domesticus", one or multiple values. Default: NULL (All).

ethnicity

The ethnicity of the datasets, choose from "Asian", "European", "unknown", "na", "African", "Bangladeshi", "British", "Irish", "East Asian", "African American", "Hispanic or Latin American", "African American or Afro-Caribbean", "European American", "Finnish", "Indian", "Japanese", "Korean", "Malaysian", "Singaporean Chinese", "American", "Pacific Islander", "admixed ancestry", "Eskimo", "Han Chinese", "Greater Middle Eastern (Middle Eastern, North African or Persian)", "multiethnic", "Jewish Israeli", "South Asian", "Oceanian", "Chinese", one or multiple values. Default: NULL (All).

sex

The sex of the datasets, choose from "female", "male", "unknown", one or multiple values. Default: NULL (All).

tissue

The tissue of the datasets, obtain available values with StatDBAttribute. One or multiple values. Default: NULL (All).

disease

The disease of the datasets, obtain available values with StatDBAttribute. One or multiple values. Default: NULL (All).

assay

The assay of the datasets, choose from "10x 3' v1", "10x 3' v2", "10x 3' v3", "10x 3' transcription profiling", "10x 5' v1", "10x 5' v2", "10x 5' transcription profiling", "10x multiome", "10x scATAC-seq", "sci-RNA-seq", "Drop-seq", "Smart-seq", "Smart-seq2", "Smart-seq v4", "snmC-Seq2", "Visium Spatial Gene Expression", "Seq-Well", "Seq-Well S3", "Patch-seq", "sci-Plex", "BD Rhapsody Targeted mRNA", "BD Rhapsody Whole Transcriptome Analysis", "Slide-seqV2", "GEXSCOPE technology", "inDrop", "microwell-seq", "CEL-seq2", "STRT-seq", "DroNc-seq", "MERFISH", "scATAC-seq", "MARS-seq", "TruDrop", one or multiple values. Default: NULL (All).

suspension.type

The suspension type of the datasets, choose from "nucleus", "cell", "na", one or multiple values. Default: NULL (All).

cell.type

The cell type of the datasets, obtain available values with StatDBAttribute. One or multiple values. Default: NULL (All).

cell.num

Cell number filter. If NULL, no filter; if one value, lower filter; if two values, low and high filter. Deault: NULL(without filtering).

References

https://gist.github.com/ivirshup/f1a1603db69de3888eacb4bdb6a9317a

Examples

# \donttest{
# all available datasets
all.cellxgene.datasets <- ShowCELLxGENEDatasets()
# human 10x v2 and v3 datasets
human.10x.cellxgene.meta <- ExtractCELLxGENEMeta(
  all.samples.df = all.cellxgene.datasets,
  assay = c("10x 3' v2", "10x 3' v3"),
  organism = "Homo sapiens"
)
# }