clustifyrdatahub provides external reference data sets for cell-type assignment with clustifyr.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clustifyrdatahub")knitr::kable(dplyr::select(
read.csv(system.file("extdata", "metadata.csv", package = "clustifyrdatahub")),
c(1, 9, 2:7)))| 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 |
clustifyrdatahublibrary(ExperimentHub)
eh <- ExperimentHub()
## query
refs <- query(eh, "clustifyrdatahub")
refs
#> ExperimentHub with 11 records
#> # snapshotDate(): 2024-04-29
#> # $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(): 2024-04-29
#> # 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"]]'sessionInfo()
#> R version 4.4.0 RC (2024-04-16 r86468)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] clustifyrdatahub_1.15.0 ExperimentHub_2.13.0 AnnotationHub_3.13.0
#> [4] BiocFileCache_2.13.0 dbplyr_2.5.0 BiocGenerics_0.51.0
#> [7] BiocStyle_2.33.0
#>
#> loaded via a namespace (and not attached):
#> [1] DBI_1.2.2 rlang_1.1.3
#> [3] magrittr_2.0.3 matrixStats_1.3.0
#> [5] compiler_4.4.0 RSQLite_2.3.6
#> [7] png_0.1-8 vctrs_0.6.5
#> [9] pkgconfig_2.0.3 crayon_1.5.2
#> [11] fastmap_1.1.1 XVector_0.45.0
#> [13] utf8_1.2.4 rmarkdown_2.26
#> [15] UCSC.utils_1.1.0 purrr_1.0.2
#> [17] bit_4.0.5 xfun_0.43
#> [19] zlibbioc_1.51.0 cachem_1.0.8
#> [21] GenomeInfoDb_1.41.0 jsonlite_1.8.8
#> [23] blob_1.2.4 DelayedArray_0.31.0
#> [25] BiocParallel_1.39.0 parallel_4.4.0
#> [27] R6_2.5.1 bslib_0.7.0
#> [29] parallelly_1.37.1 GenomicRanges_1.57.0
#> [31] jquerylib_0.1.4 Rcpp_1.0.12
#> [33] bookdown_0.39 SummarizedExperiment_1.35.0
#> [35] knitr_1.46 future.apply_1.11.2
#> [37] IRanges_2.39.0 Matrix_1.7-0
#> [39] tidyselect_1.2.1 abind_1.4-5
#> [41] yaml_2.3.8 codetools_0.2-20
#> [43] curl_5.2.1 listenv_0.9.1
#> [45] lattice_0.22-6 tibble_3.2.1
#> [47] Biobase_2.65.0 withr_3.0.0
#> [49] KEGGREST_1.45.0 evaluate_0.23
#> [51] future_1.33.2 Biostrings_2.73.0
#> [53] pillar_1.9.0 BiocManager_1.30.22
#> [55] filelock_1.0.3 MatrixGenerics_1.17.0
#> [57] clustifyr_1.17.0 stats4_4.4.0
#> [59] generics_0.1.3 sp_2.1-4
#> [61] BiocVersion_3.20.0 S4Vectors_0.43.0
#> [63] ggplot2_3.5.1 munsell_0.5.1
#> [65] scales_1.3.0 globals_0.16.3
#> [67] glue_1.7.0 tools_4.4.0
#> [69] data.table_1.15.4 fgsea_1.31.0
#> [71] dotCall64_1.1-1 fastmatch_1.1-4
#> [73] cowplot_1.1.3 grid_4.4.0
#> [75] tidyr_1.3.1 AnnotationDbi_1.67.0
#> [77] colorspace_2.1-0 SingleCellExperiment_1.27.0
#> [79] GenomeInfoDbData_1.2.12 cli_3.6.2
#> [81] rappdirs_0.3.3 spam_2.10-0
#> [83] fansi_1.0.6 S4Arrays_1.5.0
#> [85] dplyr_1.1.4 gtable_0.3.5
#> [87] sass_0.4.9 digest_0.6.35
#> [89] progressr_0.14.0 SparseArray_1.5.0
#> [91] SeuratObject_5.0.1 memoise_2.0.1
#> [93] entropy_1.3.1 htmltools_0.5.8.1
#> [95] lifecycle_1.0.4 httr_1.4.7
#> [97] mime_0.12 bit64_4.0.5