Last updated: 2025-02-22
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Knit directory: muse/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5b60bcc | Dave Tang | 2025-02-22 | Monaco reference |
| html | 5917ece | Dave Tang | 2025-02-13 | Build site. |
| Rmd | 329c881 | Dave Tang | 2025-02-13 | Pokedex for cell types |
The celldex package provides convenient access to several cell type reference datasets. Most of these references are derived from bulk RNA-seq or microarray data of cell populations that (hopefully) consist of a pure cell type after sorting and/or culturing. The aim is to provide a common resource for further analysis like cell type annotation of single cell expression data or deconvolution of cell type proportions in bulk expression datasets.
Install celldex.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("celldex")We can examine the available references using the
surveyReferences() function. This returns a DataFrame of
the reference’s name and version, along with additional information like
the title, description, species, number of samples, available labels,
and so on.
suppressPackageStartupMessages(library(celldex))
surveyReferences()DataFrame with 7 rows and 10 columns
name version path title
<character> <character> <character> <character>
1 dice 2024-02-26 NA Human bulk RNA-seq d..
2 blueprint_encode 2024-02-26 NA Human bulk RNA-seq d..
3 immgen 2024-02-26 NA Mouse microarray exp..
4 mouse_rnaseq 2024-02-26 NA Bulk RNA-seq data of..
5 hpca 2024-02-26 NA Microarray data from..
6 novershtern_hematopo.. 2024-02-26 NA Bulk microarray expr..
7 monaco_immune 2024-02-26 NA Human bulk RNA-seq d..
description taxonomy_id genome samples
<character> <List> <List> <integer>
1 Human bulk RNA-seq d.. 9606 1561
2 Human bulk RNA-seq d.. 9606 259
3 Mouse microarray exp.. 10090 830
4 Bulk RNA-seq data of.. 10090 MGSCv37 358
5 Microarray data from.. 9606 713
6 Bulk microarray expr.. 9606 211
7 Human bulk RNA-seq d.. 9606 GRCh38 114
labels
<List>
1 label.main,label.fine,label.ont
2 label.main,label.fine,label.ont
3 label.main,label.fine,label.ont
4 label.main,label.fine,label.ont
5 label.main,label.fine,label.ont
6 label.main,label.fine,label.ont
7 label.main,label.fine,label.ont
sources
<SplitDataFrameList>
1 PubMed:30449622:NA,ExperimentHub:EH3488:NA,ExperimentHub:EH3489:NA
2 PubMed:22955616:NA,PubMed:24091925:NA,PubMed:30643263:NA
3 PubMed:18800157:NA,GEO:GSE15907:NA,GEO:GSE37448:NA
4 PubMed:30858345:NA,URL:https://github.com/B..:NA,PubMed:30643263:NA
5 PubMed:24053356:NA,PubMed:30643263:NA,GitHub:dviraran/SingleR:adc4a0e4d5cfa79db18f..
6 PubMed:21241896:NA,GEO:GSE24759:NA,ExperimentHub:EH3490:NA
7 PubMed:30726743:NA,GEO:GSE107011:NA,ExperimentHub:EH3496:NAThe Monaco reference consists of bulk RNA-seq samples of sorted immune cell populations from GSE107011 (Monaco et al. 2019).
This is the human immune reference that best covers all of the bases for a typical PBMC sample. It provides expansive B and T cell subsets, differentiates between classical and non-classical monocytes, includes basic dendritic cell subsets, and also includes neutrophil and basophil samples to help identify small contaminating populations that may have slipped into a PBMC preparation.
monaco_immune <- fetchReference("monaco_immune", "2024-02-26")
colData(monaco_immune) |>
as.data.frame() label.main label.fine label.ont
DZQV_CD8_naive CD8+ T cells Naive CD8 T cells CL:0000900
DZQV_CD8_CM CD8+ T cells Central memory CD8 T cells CL:0000907
DZQV_CD8_EM CD8+ T cells Effector memory CD8 T cells CL:0000913
DZQV_CD8_TE CD8+ T cells Terminal effector CD8 T cells CL:0001062
DZQV_MAIT T cells MAIT cells CL:0000940
DZQV_VD2+ T cells Vd2 gd T cells CL:0000798
DZQV_VD2- T cells Non-Vd2 gd T cells CL:0000798
DZQV_TFH CD4+ T cells Follicular helper T cells CL:0002038
DZQV_Treg CD4+ T cells T regulatory cells CL:0000815
DZQV_Th1 CD4+ T cells Th1 cells CL:0000545
DZQV_Th1/Th17 CD4+ T cells Th1/Th17 cells CL:0000912
DZQV_Th17 CD4+ T cells Th17 cells CL:0000899
DZQV_Th2 CD4+ T cells Th2 cells CL:0000546
DZQV_CD4_naive CD4+ T cells Naive CD4 T cells CL:0000895
DZQV_Progenitor Progenitors Progenitor cells CL:0002043
DZQV_B_naive B cells Naive B cells CL:0000788
DZQV_B_NSM B cells Non-switched memory B cells CL:0000970
DZQV_B_Ex B cells Exhausted B cells CL:0000236
DZQV_B_SM B cells Switched memory B cells CL:0000972
DZQV_Plasmablasts B cells Plasmablasts CL:0000980
DZQV_C_mono Monocytes Classical monocytes CL:0000860
DZQV_I_mono Monocytes Intermediate monocytes CL:0002393
DZQV_NC_mono Monocytes Non classical monocytes CL:0000875
DZQV_NK NK cells Natural killer cells CL:0000623
DZQV_pDC Dendritic cells Plasmacytoid dendritic cells CL:0000784
DZQV_mDC Dendritic cells Myeloid dendritic cells CL:0000782
DZQV_Neutrophils Neutrophils Low-density neutrophils CL:0000096
DZQV_Basophils Basophils Low-density basophils CL:0000043
925L_CD8_naive CD8+ T cells Naive CD8 T cells CL:0000900
925L_CD8_CM CD8+ T cells Central memory CD8 T cells CL:0000907
925L_CD8_EM CD8+ T cells Effector memory CD8 T cells CL:0000913
925L_CD8_TE CD8+ T cells Terminal effector CD8 T cells CL:0001062
925L_MAIT T cells MAIT cells CL:0000940
925L_VD2+ T cells Vd2 gd T cells CL:0000798
925L_VD2- T cells Non-Vd2 gd T cells CL:0000798
925L_TFH CD4+ T cells Follicular helper T cells CL:0002038
925L_Treg CD4+ T cells T regulatory cells CL:0000815
925L_Th1 CD4+ T cells Th1 cells CL:0000545
925L_Th1/Th17 CD4+ T cells Th1/Th17 cells CL:0000912
925L_Th17 CD4+ T cells Th17 cells CL:0000899
925L_Th2 CD4+ T cells Th2 cells CL:0000546
925L_CD4_naive CD4+ T cells Naive CD4 T cells CL:0000895
925L_CD4_TE CD4+ T cells Terminal effector CD4 T cells CL:0001044
925L_Progenitor Progenitors Progenitor cells CL:0002043
925L_B_naive B cells Naive B cells CL:0000788
925L_B_NSM B cells Non-switched memory B cells CL:0000970
925L_B_Ex B cells Exhausted B cells CL:0000236
925L_B_SM B cells Switched memory B cells CL:0000972
925L_Plasmablasts B cells Plasmablasts CL:0000980
925L_C_mono Monocytes Classical monocytes CL:0000860
925L_I_mono Monocytes Intermediate monocytes CL:0002393
925L_NC_mono Monocytes Non classical monocytes CL:0000875
925L_NK NK cells Natural killer cells CL:0000623
925L_pDC Dendritic cells Plasmacytoid dendritic cells CL:0000784
925L_mDC Dendritic cells Myeloid dendritic cells CL:0000782
925L_Neutrophils Neutrophils Low-density neutrophils CL:0000096
925L_Basophils Basophils Low-density basophils CL:0000043
9JD4_CD8_naive CD8+ T cells Naive CD8 T cells CL:0000900
9JD4_CD8_CM CD8+ T cells Central memory CD8 T cells CL:0000907
9JD4_CD8_EM CD8+ T cells Effector memory CD8 T cells CL:0000913
9JD4_CD8_TE CD8+ T cells Terminal effector CD8 T cells CL:0001062
9JD4_MAIT T cells MAIT cells CL:0000940
9JD4_VD2+ T cells Vd2 gd T cells CL:0000798
9JD4_VD2- T cells Non-Vd2 gd T cells CL:0000798
9JD4_TFH CD4+ T cells Follicular helper T cells CL:0002038
9JD4_Treg CD4+ T cells T regulatory cells CL:0000815
9JD4_Th1 CD4+ T cells Th1 cells CL:0000545
9JD4_Th1/Th17 CD4+ T cells Th1/Th17 cells CL:0000912
9JD4_Th17 CD4+ T cells Th17 cells CL:0000899
9JD4_Th2 CD4+ T cells Th2 cells CL:0000546
9JD4_CD4_naive CD4+ T cells Naive CD4 T cells CL:0000895
9JD4_CD4_TE CD4+ T cells Terminal effector CD4 T cells CL:0001044
9JD4_Progenitor Progenitors Progenitor cells CL:0002043
9JD4_B_naive B cells Naive B cells CL:0000788
9JD4_B_NSM B cells Non-switched memory B cells CL:0000970
9JD4_B_Ex B cells Exhausted B cells CL:0000236
9JD4_B_SM B cells Switched memory B cells CL:0000972
9JD4_Plasmablasts B cells Plasmablasts CL:0000980
9JD4_C_mono Monocytes Classical monocytes CL:0000860
9JD4_I_mono Monocytes Intermediate monocytes CL:0002393
9JD4_NC_mono Monocytes Non classical monocytes CL:0000875
9JD4_NK NK cells Natural killer cells CL:0000623
9JD4_pDC Dendritic cells Plasmacytoid dendritic cells CL:0000784
9JD4_mDC Dendritic cells Myeloid dendritic cells CL:0000782
9JD4_Neutrophils Neutrophils Low-density neutrophils CL:0000096
9JD4_Basophils Basophils Low-density basophils CL:0000043
G4YW_CD8_naive CD8+ T cells Naive CD8 T cells CL:0000900
G4YW_CD8_CM CD8+ T cells Central memory CD8 T cells CL:0000907
G4YW_CD8_EM CD8+ T cells Effector memory CD8 T cells CL:0000913
G4YW_CD8_TE CD8+ T cells Terminal effector CD8 T cells CL:0001062
G4YW_MAIT T cells MAIT cells CL:0000940
G4YW_VD2+ T cells Vd2 gd T cells CL:0000798
G4YW_VD2- T cells Non-Vd2 gd T cells CL:0000798
G4YW_TFH CD4+ T cells Follicular helper T cells CL:0002038
G4YW_Treg CD4+ T cells T regulatory cells CL:0000815
G4YW_Th1 CD4+ T cells Th1 cells CL:0000545
G4YW_Th1/Th17 CD4+ T cells Th1/Th17 cells CL:0000912
G4YW_Th17 CD4+ T cells Th17 cells CL:0000899
G4YW_Th2 CD4+ T cells Th2 cells CL:0000546
G4YW_CD4_naive CD4+ T cells Naive CD4 T cells CL:0000895
G4YW_Progenitor Progenitors Progenitor cells CL:0002043
G4YW_B_naive B cells Naive B cells CL:0000788
G4YW_B_NSM B cells Non-switched memory B cells CL:0000970
G4YW_B_Ex B cells Exhausted B cells CL:0000236
G4YW_B_SM B cells Switched memory B cells CL:0000972
G4YW_Plasmablasts B cells Plasmablasts CL:0000980
G4YW_C_mono Monocytes Classical monocytes CL:0000860
G4YW_I_mono Monocytes Intermediate monocytes CL:0002393
G4YW_NC_mono Monocytes Non classical monocytes CL:0000875
G4YW_NK NK cells Natural killer cells CL:0000623
G4YW_pDC Dendritic cells Plasmacytoid dendritic cells CL:0000784
G4YW_mDC Dendritic cells Myeloid dendritic cells CL:0000782
G4YW_Neutrophils Neutrophils Low-density neutrophils CL:0000096
G4YW_Basophils Basophils Low-density basophils CL:0000043
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[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: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] celldex_1.16.0 SummarizedExperiment_1.36.0
[3] Biobase_2.66.0 GenomicRanges_1.58.0
[5] GenomeInfoDb_1.42.3 IRanges_2.40.1
[7] S4Vectors_0.44.0 BiocGenerics_0.52.0
[9] MatrixGenerics_1.18.1 matrixStats_1.4.1
[11] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 alabaster.se_1.6.0
[3] dplyr_1.1.4 blob_1.2.4
[5] filelock_1.0.3 Biostrings_2.74.1
[7] fastmap_1.2.0 BiocFileCache_2.14.0
[9] promises_1.3.0 digest_0.6.37
[11] lifecycle_1.0.4 alabaster.matrix_1.6.1
[13] processx_3.8.4 KEGGREST_1.46.0
[15] alabaster.base_1.6.1 RSQLite_2.3.7
[17] magrittr_2.0.3 compiler_4.4.1
[19] rlang_1.1.4 sass_0.4.9
[21] tools_4.4.1 utf8_1.2.4
[23] yaml_2.3.10 knitr_1.48
[25] S4Arrays_1.6.0 bit_4.5.0
[27] curl_5.2.3 DelayedArray_0.32.0
[29] abind_1.4-8 HDF5Array_1.34.0
[31] gypsum_1.2.0 grid_4.4.1
[33] fansi_1.0.6 ExperimentHub_2.14.0
[35] git2r_0.35.0 Rhdf5lib_1.28.0
[37] cli_3.6.3 rmarkdown_2.28
[39] crayon_1.5.3 generics_0.1.3
[41] rstudioapi_0.17.1 httr_1.4.7
[43] DelayedMatrixStats_1.28.1 rhdf5_2.50.2
[45] DBI_1.2.3 cachem_1.1.0
[47] stringr_1.5.1 zlibbioc_1.52.0
[49] parallel_4.4.1 AnnotationDbi_1.68.0
[51] BiocManager_1.30.25 XVector_0.46.0
[53] alabaster.schemas_1.6.0 vctrs_0.6.5
[55] Matrix_1.7-0 jsonlite_1.8.9
[57] callr_3.7.6 bit64_4.5.2
[59] alabaster.ranges_1.6.0 jquerylib_0.1.4
[61] glue_1.8.0 ps_1.8.1
[63] stringi_1.8.4 BiocVersion_3.20.0
[65] later_1.3.2 UCSC.utils_1.2.0
[67] tibble_3.2.1 pillar_1.9.0
[69] rhdf5filters_1.18.0 rappdirs_0.3.3
[71] htmltools_0.5.8.1 GenomeInfoDbData_1.2.13
[73] httr2_1.0.5 R6_2.5.1
[75] dbplyr_2.5.0 sparseMatrixStats_1.18.0
[77] rprojroot_2.0.4 evaluate_1.0.1
[79] lattice_0.22-6 AnnotationHub_3.14.0
[81] png_0.1-8 memoise_2.0.1
[83] httpuv_1.6.15 bslib_0.8.0
[85] Rcpp_1.0.13 SparseArray_1.6.1
[87] whisker_0.4.1 xfun_0.48
[89] fs_1.6.4 getPass_0.2-4
[91] pkgconfig_2.0.3