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SRTsim (version 0.99.7)

Simulator for Spatially Resolved Transcriptomics

Description

An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.

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Version

Install

install.packages('SRTsim')

Monthly Downloads

39

Version

0.99.7

License

GPL (>= 3)

Maintainer

Jiaqiang Zhu

Last Published

August 21st, 2024

Functions in SRTsim (0.99.7)

srtsim_newlocs

Fit the marginal distributions for each row of a count matrix
refcolData

Access reference colData
refrowData

Access reference rowData
subsetSRT

Subset SRT object based on domain labels of interest
toyData

A toyExample to showcase reference-based simulations
srtsim_count_affine

Generate Data with Estimated Parameters For A New Designed Pattern
visualize_metrics

Visualize summarized metrics for reference data and synthetic data
refCounts

Access reference count matrix
reGenCountshiny

ReSimulate Count Data with Parameters Specification from Shiny
srtsim_count

Generate Data with Estimated Parameters
visualize_gene

Visualize expression pattern for the gene of interest in reference data and synthetic data
toyShiny

A toyExample to showcase reference-free simulations
fit_pos_optim

fitting data with poisson through optim function
exampleLIBD

Data used for creating vignettes
createSRT

Create simSRT object
convert_grid

Convert continuous coordinate into integer, essential for BayesSpace to determine the neighborhood info
compareSRT

Summarize metrics for reference data and synthetic data
Shiny2SRT

Create a SRTsim object from reference-free shinyoutput
srtsim_fit

Fit the marginal distributions for each row of a count matrix
EstParam

Access Model Fitting Parameters
SRTsim_shiny

Run the SRTsim Shiny Application
get_stats_loc

Summarize location-wise summary metrics
simcolData

Access synthetic colData
simrowData

Access synthetic rowData
srtsim_cci_free

Generate Data with Cell-Cell Interaction Under Reference-Free Mode
srtsim_cci_ref

Generate Data with Cell-Cell Interaction Under Reference-Based Mode
simCounts

Access synthetic count matrix
get_metrics_pd

Extracted summarized metrics for reference data and synthetic data
get_stats_gene

Summarize gene-wise summary metrics
simNewLocs

Fit the marginal distributions for single gene
metaParam

Access User-Specified Parameters