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-4.5)GeneScape_1.2.zip(r-4.4)GeneScape_1.2.zip(r-4.3)
GeneScape_1.2.tgz(r-4.4-x86_64)GeneScape_1.2.tgz(r-4.4-arm64)GeneScape_1.2.tgz(r-4.3-x86_64)GeneScape_1.2.tgz(r-4.3-arm64)
GeneScape_1.2.tar.gz(r-4.5-noble)GeneScape_1.2.tar.gz(r-4.4-noble)
GeneScape_1.2.tgz(r-4.4-emscripten)GeneScape_1.2.tgz(r-4.3-emscripten)
GeneScape.pdf |GeneScape.html✨
GeneScape/json (API)

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

Peer review:

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

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

On CRAN:

2.00 score 2 scripts 151 downloads 34 exports 36 dependencies

Last updated 1 years agofrom:be6c631fd1. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64NOTENov 07 2024
R-4.5-linux-x86_64NOTENov 07 2024
R-4.4-win-x86_64NOTENov 07 2024
R-4.4-mac-x86_64NOTENov 07 2024
R-4.4-mac-aarch64NOTENov 07 2024
R-4.3-win-x86_64NOTENov 07 2024
R-4.3-mac-x86_64NOTENov 07 2024
R-4.3-mac-aarch64NOTENov 07 2024

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:classclassIntcliconcavemancorpcorcurlDBIdplyre1071fansigenericsgluejsonliteKernSmoothlamWlifecyclemagrittrMASSpillarpkgconfigproxyR6RcppRcppArmadilloRcppParallelrlangs2sftibbletidyselectunitsutf8V8vctrswithrwk

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