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STexampleData package:STexampleData R Documentation
_C_o_l_l_e_c_t_i_o_n _o_f _s_p_a_t_i_a_l _t_r_a_n_s_c_r_i_p_t_o_m_i_c_s _d_a_t_a_s_e_t_s _i_n _S_p_a_t_i_a_l_E_x_p_e_r_i_m_e_n_t
_B_i_o_c_o_n_d_u_c_t_o_r _f_o_r_m_a_t
_D_e_s_c_r_i_p_t_i_o_n:
Collection of spatial transcriptomics datasets in
SpatialExperiment Bioconductor format, for use in examples,
demonstrations, and tutorials. The datasets are from several
different technological platforms and have been sourced from
various publicly available sources. Several datasets include
images and/or reference annotation labels.
_D_e_t_a_i_l_s:
The 'STexampleData' package contains a collection of spatial
transcriptomics datasets, which have been formatted into the
'SpatialExperiment' Bioconductor class, for use in examples,
demonstrations, and tutorials.
The datasets are from several different technological platforms
and have been sourced from various publicly available sources.
Several datasets include images and/or reference annotation
labels.
Additional examples and documentation are provided in the package
vignette.
_Datasets_
The 'STexampleData' package contains the following datasets:
• Visium_humanDLPFC (10x Genomics Visium): A single sample
(sample 151673) of human brain dorsolateral prefrontal cortex
(DLPFC) in the human brain, measured using the 10x Genomics
Visium platform. This is a subset of the full dataset
containing 12 samples from 3 neurotypical donors, published
by Maynard and Collado-Torres et al. (2021). The full dataset
is available from the 'spatialLIBD' Bioconductor package.
• Visium_mouseCoronal (10x Genomics Visium): A single coronal
section from the mouse brain, spanning one hemisphere. This
dataset was previously released by 10x Genomics on their
website.
• seqFISH_mouseEmbryo (seqFISH): A subset of cells (embryo 1,
z-slice 2) from a previously published dataset investigating
mouse embryogenesis by Lohoff and Ghazanfar et al. (2022),
generated using the seqFISH platform. The full dataset is
available from the original publication.
• ST_mouseOB (Spatial Transcriptomics): A single sample from
the mouse brain olfactory bulb (OB), measured with the
Spatial Transcriptomics platform (Stahl et al. 2016). This
dataset contains annotations for five cell layers from the
original authors.
• SlideSeqV2_mouseHPC (Slide-seqV2): A single sample of mouse
brain from the hippocampus (HPC) and surrounding regions,
measured with the Slide-seqV2 platform (Stickels et al.
2021). This dataset contains cell type annotations generated
by Cable et al. (2022).
• Janesick_breastCancer_Chromium (10x Genomics Chromium): 10x
Genomics Chromium single-cell RNA sequencing data from human
breast cancer dataset by Janesick et al. (2023). High
resolution mapping of the breast cancer tumor
microenvironment using integrated single-cell, spatial, and
in situ analysis of FFPE tissue. Contains annotations for
cell type from the original authors.
• Janesick_breastCancer_Visium (10x Genomics Visium): 10x
Genomics Visium spatial transcriptomics data from human
breast cancer dataset by Janesick et al. (2023). High
resolution mapping of the breast cancer tumor
microenvironment using integrated single-cell, spatial, and
in situ analysis of FFPE tissue.
• Janesick_breastCancer_Xenium_rep1 (10x Genomics Xenium): 10x
Genomics Xenium in situ spatial data (sample 1, replicate 1)
from human breast cancer dataset by Janesick et al. (2023).
High resolution mapping of the breast cancer tumor
microenvironment using integrated single-cell, spatial, and
in situ analysis of FFPE tissue.
• Janesick_breastCancer_Xenium_rep2 (10x Genomics Xenium): 10x
Genomics Xenium in situ spatial data (sample 1, replicate 2)
from human breast cancer dataset by Janesick et al. (2023).
High resolution mapping of the breast cancer tumor
microenvironment using integrated single-cell, spatial, and
in situ analysis of FFPE tissue.
• CosMx_lungCancer (NanoString CosMx): NanoString CosMx human
non-small cell lung cancer (NSCLC) dataset. Contains data
from one sample (patient 9, slice 1). This dataset was
previously released by NanoString on their website.
• MERSCOPE_ovarianCancer (Vizgen MERSCOPE): Vizgen MERSCOPE
human ovarian cancer dataset. Contains data from one sample
(patient 2, sample 1). This dataset was previously released
by Vizgen on their website.
• STARmapPLUS_mouseBrain (STARmap PLUS): STARmap PLUS mouse
brain data by Shi et al. (2023). Contains data from one
sample (well 05), including annotations for cell type and
tissue regions from the original authors.
_E_x_a_m_p_l_e_s:
# load using dataset name
spe <- Visium_humanDLPFC()
spe
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[31mError: package or namespace load failed for 'imcRtools' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'beachmat'
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<error/rlang_error>
Error:
! package or namespace load failed for 'imcRtools' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'beachmat'
---
Backtrace:
▆
1. └─base::library(imcRtools)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted