Package: GeneScape 1.2

Qi Gao

GeneScape: Simulate single cell and spatial transcriptomics data

Simulate single cell and spatial transcriptomics data with complicated heterogeneity structure with or without reference dataset.

Authors:Qi Gao

GeneScape_1.2.tar.gz
GeneScape_1.2.zip(r-4.7)GeneScape_1.2.zip(r-4.6)GeneScape_1.2.zip(r-4.5)
GeneScape_1.2.tgz(r-4.6-x86_64)GeneScape_1.2.tgz(r-4.6-arm64)GeneScape_1.2.tgz(r-4.5-x86_64)GeneScape_1.2.tgz(r-4.5-arm64)
GeneScape_1.2.tar.gz(r-4.7-arm64)GeneScape_1.2.tar.gz(r-4.7-x86_64)GeneScape_1.2.tar.gz(r-4.6-arm64)GeneScape_1.2.tar.gz(r-4.6-x86_64)
GeneScape_1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GeneScape/json (API)

# Install 'GeneScape' in R:
install.packages('GeneScape', repos = c('https://qigao1.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/qigao1/genescape/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

cppopenmp

2.00 score 2 scripts 120 downloads 34 exports 20 dependencies

Last updated from:be6c631fd1. Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE131
linux-devel-x86_64NOTE137
source / vignettesOK198
linux-release-arm64NOTE145
linux-release-x86_64NOTE165
macos-release-arm64NOTE198
macos-release-x86_64NOTE226
macos-oldrel-arm64NOTE188
macos-oldrel-x86_64NOTE249
windows-develNOTE132
windows-releaseNOTE121
windows-oldrelNOTE140
wasm-releaseOK123

Exports:add_distortaggregate_expressionassign_cell_typesassign_tissue_typescell_position_simulationchangeLibSizecumsum_cppdownSampleReadest_boundestimate_gammaestimate_lognormalestimate_nbestimate_zinbestimate_zipfcsimGeneScape_estGeneScape_parGeneScape_simGeneScapeS_estGeneScapeS_siminverse_logitknn_tissue_updateknnassignrotate_pgrotate_samplesample_intsample_region_simulationscale_sampleshift_samplesp_dist_euclidean_cppspot_simulatetissue_region_simulationupdate_sample_regionzinb_nll

Dependencies:classclassIntconcavemancorpcorcurlDBIe1071jsonliteKernSmoothlamWMASSproxyRcppRcppArmadilloRcppParallels2sfunitsV8wk

Readme and manuals

Help Manual

Help pageTopics
add_distortadd_distort
aggregate_expressionaggregate_expression
assign_cell_typesassign_cell_types
assign_tissue_typesassign_tissue_types
cell_position_simulationcell_position_simulation
changeLibSize This function modifies the simulated counts so that the total read count in each spot is the same as the example data.changeLibSize
cumsum_cpp This function calculates the cumulative sum (partial sum) of a vector.cumsum_cpp
downSampleRead This function uses down-sampling to obtain the reads in each spot.downSampleRead
est_boundest_bound
estimate_gamma This function estimates gamma distribution shape and rate parameters.estimate_gamma
estimate_lognormal This function estimates estimate_lognormal distribution loc and scale parameters.estimate_lognormal
estimate_nb This function estimates negative binomial distribution mean and dispersion parameters.estimate_nb
estimate_zinb This function estimates the mean, dispersion and zero inflation parameters in zero-inflated negative binomial distribution.estimate_zinb
estimate_zipestimate_zip
fcsimfcsim
GeneScape_estGeneScape_est
GeneScape_parGeneScape_par
GeneScape_simGeneScape_sim
GeneScapeS_est This function estimates distribution parameters from an example data.GeneScapeS_est
GeneScapeS_sim This function generates simulated data based on distribution parameters estimated from an example data.GeneScapeS_sim
inverse_logit This function is the inverse logit function.inverse_logit
knn_tissue_updateknn_tissue_update
knnassign This function uses KNN sampling to simulate gradually changed tissue types.knnassign
rotate_pgrotate_pg
rotate_samplerotate_sample
sample_int This function samples integers from 1 to an upper limit integer value with equal probability without replacement.sample_int
sample_region_simulationsample_region_simulation
scale_samplescale_sample
shift_sampleshift_sample
sp_dist_euclidean_cpp This function calculates Euclidean distance between cell locations and spot locations.sp_dist_euclidean_cpp
spot_simulatespot_simulate
tissue_region_simulationtissue_region_simulation
update_sample_regionupdate_sample_region
zinb_nll This function calculates the negative log likelihood of zero-inflated negative binomial distribution.zinb_nll