README.md

In rnabioco/clustifyrdatahub: External data sets for clustifyr in ExperimentHub

clustifyrdatahub

clustifyrdatahub provides external reference data sets for cell-type assignment with clustifyr.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clustifyrdatahub")

Available references include

| Title | Species | Description | RDataPath | BiocVersion | Genome | SourceType | SourceUrl | |:----------------------|:-------------|:-------------------------------------------------|:-------------------------------------------|------------:|:-------|:-----------|:-----------------------------------------------------------------------------------------------------| | ref_MCA | Mus musculus | Mouse Cell Atlas | clustifyrdatahub/ref_MCA.rda | 3.12 | mm10 | Zip | https://ndownloader.figshare.com/files/10756795 | | ref_tabula_muris_drop | Mus musculus | Tabula Muris (10X) | clustifyrdatahub/ref_tabula_muris_drop.rda | 3.12 | mm10 | Zip | https://ndownloader.figshare.com/articles/5821263 | | ref_tabula_muris_facs | Mus musculus | Tabula Muris (SmartSeq2) | clustifyrdatahub/ref_tabula_muris_facs.rda | 3.12 | mm10 | Zip | https://ndownloader.figshare.com/articles/5821263 | | ref_mouse.rnaseq | Mus musculus | Mouse RNA-seq from 28 cell types | clustifyrdatahub/ref_mouse.rnaseq.rda | 3.12 | mm10 | RDA | https://github.com/dviraran/SingleR/tree/master/data | | ref_moca_main | Mus musculus | Mouse Organogenesis Cell Atlas (main cell types) | clustifyrdatahub/ref_moca_main.rda | 3.12 | mm10 | RDA | https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads | | ref_immgen | Mus musculus | Mouse sorted immune cells | clustifyrdatahub/ref_immgen.rda | 3.12 | mm10 | RDA | https://github.com/dviraran/SingleR/tree/master/data | | ref_hema_microarray | Homo sapiens | Human hematopoietic cell microarray | clustifyrdatahub/ref_hema_microarray.rda | 3.12 | hg38 | TXT | https://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24759/matrix/GSE24759_series_matrix.txt.gz | | ref_cortex_dev | Homo sapiens | Human cortex development scRNA-seq | clustifyrdatahub/ref_cortex_dev.rda | 3.12 | hg38 | TSV | https://cells.ucsc.edu/cortex-dev/exprMatrix.tsv.gz | | ref_pan_indrop | Homo sapiens | Human pancreatic cell scRNA-seq (inDrop) | clustifyrdatahub/ref_pan_indrop.rda | 3.12 | hg38 | RDA | https://scrnaseq-public-datasets.s3.amazonaws.com/scater-objects/baron-human.rds | | ref_pan_smartseq2 | Homo sapiens | Human pancreatic cell scRNA-seq (SmartSeq2) | clustifyrdatahub/ref_pan_smartseq2.rda | 3.12 | hg38 | RDA | https://scrnaseq-public-datasets.s3.amazonaws.com/scater-objects/segerstolpe.rds | | ref_mouse_atlas | Mus musculus | Mouse Atlas scRNA-seq from 321 cell types | clustifyrdatahub/ref_mouse_atlas.rda | 3.12 | mm10 | RDA | https://github.com/rnabioco/scRNA-seq-Cell-Ref-Matrix/blob/master/atlas/musMusculus/MouseAtlas.rda |

To use clustifyrdatahub

library(ExperimentHub)
eh <- ExperimentHub()

## query
refs <- query(eh, "clustifyrdatahub")
refs
#> ExperimentHub with 11 records
#> # snapshotDate(): 2022-04-26
#> # $dataprovider: figshare, S3, GitHub, GEO, washington.edu, UCSC
#> # $species: Mus musculus, Homo sapiens
#> # $rdataclass: data.frame
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["EH3444"]]' 
#> 
#>            title                
#>   EH3444 | ref_MCA              
#>   EH3445 | ref_tabula_muris_drop
#>   EH3446 | ref_tabula_muris_facs
#>   EH3447 | ref_mouse.rnaseq     
#>   EH3448 | ref_moca_main        
#>   ...      ...                  
#>   EH3450 | ref_hema_microarray  
#>   EH3451 | ref_cortex_dev       
#>   EH3452 | ref_pan_indrop       
#>   EH3453 | ref_pan_smartseq2    
#>   EH3779 | ref_mouse_atlas
## either by index or id
ref_hema_microarray <- refs[[7]]         ## load the first resource in the list
ref_hema_microarray <- refs[["EH3450"]]  ## load by EH id

## or list and load
refs <- listResources(eh, "clustifyrdatahub")
ref_hema_microarray <- loadResources(eh, "clustifyrdatahub", "ref_hema_microarray")[[1]]

## use for classification of cell types
res <- clustifyr::clustify(
  input = clustifyr::pbmc_matrix_small,
  metadata = clustifyr::pbmc_meta$classified,
  ref_mat = ref_hema_microarray,
  query_genes = clustifyr::pbmc_vargenes
)

## or load refs by function name (after loading hub library)
library(clustifyrdatahub)
ref_hema_microarray()[1:5, 1:5]           ## data are loaded
#>        Basophils CD4+ Central Memory CD4+ Effector Memory CD8+ Central Memory
#> DDR1    6.084244            5.967502             5.933039            6.005278
#> RFC2    6.280044            6.028615             6.047005            5.992979
#> HSPA6   6.535444            5.811475             5.746326            5.928349
#> PAX8    6.669153            5.896401             6.118577            6.270870
#> GUCA1A  5.239230            5.232116             5.206960            5.227415
#>        CD8+ Effector Memory
#> DDR1               5.895926
#> RFC2               5.942426
#> HSPA6              5.942670
#> PAX8               6.323922
#> GUCA1A             5.090882
ref_hema_microarray(metadata = TRUE)       ## only metadata
#> ExperimentHub with 1 record
#> # snapshotDate(): 2022-04-26
#> # names(): EH3450
#> # package(): clustifyrdatahub
#> # $dataprovider: GEO
#> # $species: Homo sapiens
#> # $rdataclass: data.frame
#> # $rdatadateadded: 2020-05-14
#> # $title: ref_hema_microarray
#> # $description: Human hematopoietic cell microarray
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: TXT
#> # $sourceurl: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE24nnn/GSE24759/matr...
#> # $sourcesize: NA
#> # $tags: c("SingleCellData", "SequencingData", "MicroarrayData",
#> #   "ExperimentHub") 
#> # retrieve record with 'object[["EH3450"]]'

Data sets have uniform suffixes: - ref_* : the prebuilt reference expression matrix.

rnabioco/clustifyrdatahub documentation built on Nov. 11, 2023, 4:21 a.m.