Package: clustifyrdatahub 1.23.0

Kent Riemondy

clustifyrdatahub: External data sets for clustifyr in ExperimentHub

References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr <https://bioconductor.org/packages/clustifyr> to assign cell type identities.

Authors:Rui Fu [aut], Kent Riemondy [aut, cre], RNA Bioscience Initiative [fnd], Austin Gillen [ctb], Jay Hesselberth [ctb], Sidhant Puntambekar [ctb]

clustifyrdatahub_1.23.0.tar.gz
clustifyrdatahub_1.23.0.tar.gz(r-4.7-any)clustifyrdatahub_1.23.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clustifyrdatahub/json (API)

# Install 'clustifyrdatahub' in R:

install.packages('clustifyrdatahub', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rnabioco/clustifyrdatahub/issues

Pkgdown/docs site:https://rnabioco.github.io

On BioConductor:clustifyrdatahub-1.23.0(data/experiment 3.24)clustifyrdatahub-1.22.0(data/experiment 3.23)

singlecelldata sequencingdata microarraydata experimenthub rnaseqdata packagetypedata expressiondata rna-seq-analysis single-cell single-cell-rna-seq datapkg

5.99 score 9 stars 18 scripts 11 exports 57 dependencies

Last updated from:61513ac7a0. Checks:3 NOTE, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	187
linux-devel	NOTE	292
source / vignettes	OK	260
linux-release	NOTE	360

Exports:ref_cortex_dev ref_hema_microarray ref_immgen ref_MCA ref_moca_main ref_mouse_atlas ref_mouse.rnaseq ref_pan_indrop ref_pan_smartseq2 ref_tabula_muris_drop ref_tabula_muris_facs

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics glue httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png purrr R6 rappdirs rlang RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

clustifyrdatahub

Installation | Available references include | To use clustifyrdatahub | session info

Rendered fromclustifyrdatahub.Rmdusingknitr::rmarkdown

Last update: 2020-08-14
Started: 2020-06-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Matrix of average gene detection on cortex development cell types	ref_cortex_dev
Matrix of average gene detection by microarray on sorted immune cell populations	ref_hema_microarray
Matrix of average gene expression from immgen data	ref_immgen
Matrix of average gene expression for single-cell RNA-seq.	ref_MCA
Matrix of average gene expression per cluster from single-cell sci-RNA-seq3 from Mouse Organogenesis Cell Atlas.	ref_moca_main
Atlas matrix of average gene expression aggregated from scRNA-seq data of mouse organisms	ref_mouse_atlas
Matrix of average gene expression from general mouse cell type data	ref_mouse.rnaseq
Matrix of average gene expression per cluster from single-cell RNA-seq pancreas data using indrop method.	ref_pan_indrop
Matrix of average gene expression per cluster from single-cell RNA-seq pancreas data using smartseq2 method.	ref_pan_smartseq2
Matrix of average gene expression per cluster from single-cell RNA-seq from Tabula Muris (10x genomics).	ref_tabula_muris_drop
Matrix of average gene expression per cluster from single-cell RNA-seq from Tabula Muris (SMART-Seq2).	ref_tabula_muris_facs