This performs an analysis of the mouse haematopoietic stem cell (HSC) dataset generated with MARS-seq Paul et al., 2015. Cells were extracted from multiple mice under different experimental conditions (i.e., sorting protocols) and libraries were prepared using a series of 384-well plates.
library(scRNAseq)
sce.paul <- PaulHSCData(ensembl=TRUE)library(AnnotationHub)
ens.mm.v97 <- AnnotationHub()[["AH73905"]]
anno <- select(ens.mm.v97, keys=rownames(sce.paul),
keytype="GENEID", columns=c("SYMBOL", "SEQNAME"))
rowData(sce.paul) <- anno[match(rownames(sce.paul), anno$GENEID),]After loading and annotation, we inspect the resulting SingleCellExperiment object:
sce.paulclass: SingleCellExperiment
dim: 17483 10368
metadata(0):
assays(1): counts
rownames(17483): ENSMUSG00000007777 ENSMUSG00000107002 ... ENSMUSG00000039068
ENSMUSG00000064363
rowData names(3): GENEID SYMBOL SEQNAME
colnames(10368): W29953 W29954 ... W76335 W76336
colData names(13): Well_ID Seq_batch_ID ... CD34_measurement FcgR3_measurement
reducedDimNames(0):
altExpNames(0):dir.create("output",showWarnings = FALSE)
saveRDS(sce.paul,"output/paul_import_sce.RDS")Computation Started: 2023-07-21 16:23:20
Finished in 31.67 secs
Git Log
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Packages
| package | version | date |
|---|---|---|
| MatrixGenerics | 1.2.0 | 2020-10-28 |
| Biobase | 2.50.0 | 2020-10-28 |
| httr | 1.4.2 | 2020-07-23 |
| bit64 | 4.0.5 | 2020-08-31 |
| AnnotationHub | 2.22.0 | 2020-10-28 |
| shiny | 1.5.0 | 2020-07-16 |
| assertthat | 0.2.1 | 2020-07-15 |
| askpass | 1.1 | 2020-07-15 |
| interactiveDisplayBase | 1.28.0 | 2020-10-28 |
| BiocManager | 1.30.10 | 2020-07-15 |
| stats4 | 4.0.1 | 2020-06-07 |
| BiocFileCache | 1.14.0 | 2020-10-28 |
| grDevices | 4.0.1 | 2020-06-07 |
| blob | 1.2.1 | 2020-07-15 |
| Rsamtools | 2.6.0 | 2020-10-28 |
| GenomeInfoDbData | 1.2.4 | 2020-11-03 |
| yaml | 2.2.1 | 2020-07-15 |
| progress | 1.2.2 | 2020-07-15 |
| BiocVersion | 3.12.0 | 2020-05-15 |
| pillar | 1.6.0 | 2021-04-14 |
| RSQLite | 2.2.2 | 2021-01-09 |
| lattice | 0.20-41 | 2020-06-07 |
| glue | 1.4.2 | 2020-08-28 |
| base | 4.0.1 | 2020-06-07 |
| digest | 0.6.27 | 2020-10-25 |
| GenomicRanges | 1.42.0 | 2020-10-28 |
| promises | 1.1.1 | 2020-07-16 |
| XVector | 0.30.0 | 2020-10-29 |
| htmltools | 0.5.5 | 2023-07-17 |
| httpuv | 1.5.5 | 2021-01-13 |
| Matrix | 1.2-18 | 2020-06-07 |
| XML | 3.99-0.5 | 2020-07-24 |
| pkgconfig | 2.0.3 | 2020-07-15 |
| biomaRt | 2.46.0 | 2020-10-28 |
| zlibbioc | 1.36.0 | 2020-10-29 |
| purrr | 0.3.4 | 2020-07-15 |
| xtable | 1.8-4 | 2020-07-15 |
| later | 1.1.0.1 | 2020-07-15 |
| BiocParallel | 1.24.1 | 2020-11-07 |
| git2r | 0.28.0 | 2021-01-11 |
| openssl | 1.4.3 | 2020-09-19 |
| tibble | 3.1.1 | 2021-04-19 |
| AnnotationFilter | 1.14.0 | 2020-10-28 |
| generics | 0.1.0 | 2020-11-01 |
| datasets | 4.0.1 | 2020-06-07 |
| IRanges | 2.24.1 | 2020-12-13 |
| ellipsis | 0.3.1 | 2020-07-15 |
| withr | 2.4.2 | 2021-04-19 |
| cachem | 1.0.3 | 2021-02-05 |
| SummarizedExperiment | 1.20.0 | 2020-10-28 |
| GenomicFeatures | 1.42.1 | 2020-11-12 |
| lazyeval | 0.2.2 | 2020-07-15 |
| BiocGenerics | 0.36.0 | 2020-10-28 |
| cli | 2.5.0 | 2021-04-27 |
| magrittr | 2.0.1 | 2020-11-18 |
| crayon | 1.4.1 | 2021-02-09 |
| mime | 0.9 | 2020-07-15 |
| memoise | 2.0.1 | 2021-11-27 |
| evaluate | 0.14 | 2020-06-15 |
| methods | 4.0.1 | 2020-06-07 |
| fansi | 0.4.2 | 2021-01-16 |
| xml2 | 1.3.2 | 2020-07-15 |
| utils | 4.0.1 | 2020-06-07 |
| tools | 4.0.1 | 2020-06-07 |
| scRNAseq | 2.4.0 | 2020-11-10 |
| prettyunits | 1.1.1 | 2020-07-15 |
| hms | 1.0.0 | 2021-01-14 |
| lifecycle | 1.0.0 | 2021-02-16 |
| matrixStats | 0.57.0 | 2020-09-26 |
| stringr | 1.4.0 | 2020-07-15 |
| S4Vectors | 0.28.1 | 2020-12-10 |
| DelayedArray | 0.16.0 | 2020-10-28 |
| ensembldb | 2.14.0 | 2020-10-28 |
| AnnotationDbi | 1.52.0 | 2020-10-28 |
| stats | 4.0.1 | 2020-06-07 |
| Biostrings | 2.58.0 | 2020-10-28 |
| compiler | 4.0.1 | 2020-06-07 |
| GenomeInfoDb | 1.26.2 | 2020-12-09 |
| rlang | 1.1.1 | 2023-07-17 |
| grid | 4.0.1 | 2020-06-07 |
| RCurl | 1.98-1.2 | 2020-07-15 |
| graphics | 4.0.1 | 2020-06-07 |
| rappdirs | 0.3.1 | 2020-07-15 |
| SingleCellExperiment | 1.12.0 | 2020-10-28 |
| bitops | 1.0-6 | 2020-07-15 |
| ExperimentHub | 1.16.0 | 2020-10-28 |
| DBI | 1.1.1 | 2021-01-16 |
| curl | 4.3 | 2020-06-15 |
| R6 | 2.5.0 | 2020-10-29 |
| GenomicAlignments | 1.26.0 | 2020-10-28 |
| rtracklayer | 1.50.0 | 2020-10-28 |
| knitr | 1.30 | 2020-09-23 |
| dplyr | 1.0.5 | 2021-03-06 |
| fastmap | 1.1.1 | 2023-07-17 |
| bit | 4.0.4 | 2020-08-04 |
| utf8 | 1.1.4 | 2020-07-15 |
| ProtGenerics | 1.22.0 | 2020-10-28 |
| stringi | 1.5.3 | 2020-09-10 |
| parallel | 4.0.1 | 2020-06-07 |
| Rcpp | 1.0.6 | 2021-01-16 |
| vctrs | 0.3.6 | 2020-12-18 |
| dbplyr | 2.1.1 | 2021-04-07 |
| tidyselect | 1.1.0 | 2020-07-15 |
| xfun | 0.39 | 2023-07-17 |
System Information
| systemInfo | |
|---|---|
| version | R version 4.0.1 (2020-06-06) |
| platform | x86_64-apple-darwin17.0 (64-bit) |
| locale | en_CA.UTF-8 |
| OS | macOS 10.16 |
| UI | X11 |
Scikick Configuration
cat scikick.yml### Scikick Project Workflow Configuration File
# Directory where Scikick will store all standard notebook outputs
reportdir: report
# --- Content below here is best modified by using the Scikick CLI ---
# Notebook Execution Configuration (format summarized below)
# analysis:
# first_notebook.Rmd:
# second_notebook.Rmd:
# - first_notebook.Rmd # must execute before second_notebook.Rmd
# - functions.R # file is used by second_notebook.Rmd
#
# Each analysis item is executed to generate md and html files, E.g.:
# 1. <reportdir>/out_md/first_notebook.md
# 2. <reportdir>/out_html/first_notebook.html
analysis: !!omap
- index.Rmd:
- notebooks/nestorowa/import.Rmd:
- notebooks/nestorowa/quality_control.Rmd:
- notebooks/nestorowa/import.Rmd
- notebooks/nestorowa/normalization.Rmd:
- notebooks/nestorowa/quality_control.Rmd
- notebooks/nestorowa/further_exploration.Rmd:
- notebooks/nestorowa/normalization.Rmd
- notebooks/grun/import.Rmd:
- notebooks/grun/quality_control.Rmd:
- notebooks/grun/import.Rmd
- notebooks/grun/normalization.Rmd:
- notebooks/grun/quality_control.Rmd
- notebooks/grun/further_exploration.Rmd:
- notebooks/grun/normalization.Rmd
- notebooks/paul/import.Rmd:
- notebooks/paul/quality_control.Rmd:
- notebooks/paul/import.Rmd
- notebooks/paul/normalization.Rmd:
- notebooks/paul/quality_control.Rmd
- notebooks/paul/further_exploration.Rmd:
- notebooks/paul/normalization.Rmd
- notebooks/merged/merge.Rmd:
- notebooks/grun/quality_control.Rmd
- notebooks/paul/quality_control.Rmd
- notebooks/nestorowa/normalization.Rmd
- notebooks/merged/combined_analysis.Rmd:
- notebooks/merged/merge.Rmd
version_info:
snakemake: 6.0.2
ruamel.yaml: 0.16.12
scikick: 0.2.1
# Optional site theme customization
output:
BiocStyle::html_document:
code_folding: hide
theme: readable
toc_float: true
toc: true
number_sections: false
toc_depth: 5
self_contained: trueFunctions