Last updated: 2025-02-23
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Knit directory: muse/
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| Rmd | 4a2d928 | Dave Tang | 2025-02-23 | Trajectory analysis |
Install scRNAseq.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scRNAseq")
BiocManager::install("AnnotationHub")Mouse haematopoietic stem cell (HSC) dataset generated with Smart-seq2 (Nestorowa et al. 2016).
suppressPackageStartupMessages(library(scRNAseq))
sce.nest <- NestorowaHSCData()loading from cacherequire("ensembldb")suppressPackageStartupMessages(library(AnnotationHub))
ens.mm.v97 <- AnnotationHub()[["AH73905"]]loading from cacheanno <- select(ens.mm.v97, keys=rownames(sce.nest),
keytype="GENEID", columns=c("SYMBOL", "SEQNAME"))
rowData(sce.nest) <- anno[match(rownames(sce.nest), anno$GENEID),]
sce.nestclass: SingleCellExperiment
dim: 46078 1920
metadata(0):
assays(1): counts
rownames(46078): ENSMUSG00000000001 ENSMUSG00000000003 ...
ENSMUSG00000107391 ENSMUSG00000107392
rowData names(3): GENEID SYMBOL SEQNAME
colnames(1920): HSPC_007 HSPC_013 ... Prog_852 Prog_810
colData names(9): gate broad ... projected metrics
reducedDimNames(1): diffusion
mainExpName: endogenous
altExpNames(2): ERCC FACS
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] AnnotationHub_3.14.0 BiocFileCache_2.14.0
[3] dbplyr_2.5.0 ensembldb_2.30.0
[5] AnnotationFilter_1.30.0 GenomicFeatures_1.58.0
[7] AnnotationDbi_1.68.0 scRNAseq_2.20.0
[9] SingleCellExperiment_1.28.1 SummarizedExperiment_1.36.0
[11] Biobase_2.66.0 GenomicRanges_1.58.0
[13] GenomeInfoDb_1.42.3 IRanges_2.40.1
[15] S4Vectors_0.44.0 BiocGenerics_0.52.0
[17] MatrixGenerics_1.18.1 matrixStats_1.4.1
[19] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 httr2_1.0.5
[4] rlang_1.1.4 magrittr_2.0.3 git2r_0.35.0
[7] gypsum_1.2.0 compiler_4.4.1 RSQLite_2.3.7
[10] getPass_0.2-4 png_0.1-8 callr_3.7.6
[13] vctrs_0.6.5 ProtGenerics_1.38.0 stringr_1.5.1
[16] pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[19] XVector_0.46.0 utf8_1.2.4 Rsamtools_2.22.0
[22] promises_1.3.0 rmarkdown_2.28 UCSC.utils_1.2.0
[25] ps_1.8.1 purrr_1.0.2 bit_4.5.0
[28] xfun_0.48 zlibbioc_1.52.0 cachem_1.1.0
[31] jsonlite_1.8.9 blob_1.2.4 later_1.3.2
[34] rhdf5filters_1.18.0 DelayedArray_0.32.0 Rhdf5lib_1.28.0
[37] BiocParallel_1.40.0 parallel_4.4.1 R6_2.5.1
[40] bslib_0.8.0 stringi_1.8.4 rtracklayer_1.66.0
[43] jquerylib_0.1.4 Rcpp_1.0.13 knitr_1.48
[46] httpuv_1.6.15 Matrix_1.7-0 tidyselect_1.2.1
[49] rstudioapi_0.17.1 abind_1.4-8 yaml_2.3.10
[52] codetools_0.2-20 curl_5.2.3 processx_3.8.4
[55] alabaster.sce_1.6.0 lattice_0.22-6 tibble_3.2.1
[58] withr_3.0.2 KEGGREST_1.46.0 evaluate_1.0.1
[61] alabaster.schemas_1.6.0 ExperimentHub_2.14.0 Biostrings_2.74.1
[64] pillar_1.9.0 BiocManager_1.30.25 filelock_1.0.3
[67] whisker_0.4.1 generics_0.1.3 rprojroot_2.0.4
[70] RCurl_1.98-1.16 BiocVersion_3.20.0 alabaster.base_1.6.1
[73] alabaster.ranges_1.6.0 glue_1.8.0 lazyeval_0.2.2
[76] alabaster.matrix_1.6.1 tools_4.4.1 BiocIO_1.16.0
[79] GenomicAlignments_1.42.0 fs_1.6.4 XML_3.99-0.17
[82] rhdf5_2.50.2 grid_4.4.1 GenomeInfoDbData_1.2.13
[85] HDF5Array_1.34.0 restfulr_0.0.15 cli_3.6.3
[88] rappdirs_0.3.3 fansi_1.0.6 S4Arrays_1.6.0
[91] dplyr_1.1.4 alabaster.se_1.6.0 sass_0.4.9
[94] digest_0.6.37 SparseArray_1.6.1 rjson_0.2.23
[97] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[100] httr_1.4.7 mime_0.12 bit64_4.5.2