Files in bowang-lab/simATAC
This package is a single-cell ATAC-seq simulator
.gitignore
Analysis/Benchmarking/simATAC_analysis_clustering.R
Analysis/Benchmarking/simATAC_analysis_correlation.R
Analysis/Benchmarking/simATAC_analysis_peak_calling1.R
Analysis/Benchmarking/simATAC_analysis_stats.R
Analysis/Benchmarking/simATAC_benchmark_Buenrostro2018.R
Analysis/Benchmarking/simATAC_benchmark_Cusanovich2018.R
Analysis/Benchmarking/simATAC_benchmark_PBMCs.R
Analysis/Benchmarking/simATAC_clustering_metric.ipynb
Analysis/Benchmarking/simATAC_plot_evaluation.R
Analysis/Benchmarking/simATAC_simualtion_functions.R
Analysis/Modelling/Bin_polynomial_modelling.R
Analysis/Modelling/Library_size_modelling.R
Benchmarking_Data/README.md
Benchmarking_Data/hg19_genome_coordinates.txt
Benchmarking_Data/hg38_genome_coordinates.txt
Benchmarking_Data/mm10_genome_coordinates.txt
Benchmarking_Data/mm9_genome_coordinates.txt
DESCRIPTION
Docs/Bin_sparsity_boxplot_1000_noise0.png
Docs/Bin_sparsity_boxplot_288_noise0.3.png
Docs/Bin_sparsity_boxplot_288_noise0.png
Docs/Cell_sparsity_boxplot_1000_noise0.png
Docs/Cell_sparsity_boxplot_288_noise0.3.png
Docs/Cell_sparsity_boxplot_288_noise0.png
Docs/Library_size_boxplot_1000_noise0.png
Docs/Library_size_boxplot_288_noise0.3.png
Docs/Library_size_boxplot_288_noise0.png
Docs/Real_bin_mean_and_nonzero_proportion_1000_noise0.png
Docs/Real_bin_mean_and_nonzero_proportion_288_noise0.3.png
Docs/Real_bin_mean_and_nonzero_proportion_288_noise0.png
Docs/Simulated_bin_mean_and_nonzero_proportion_1000_noise0.png
Docs/Simulated_bin_mean_and_nonzero_proportion_288_noise0.3.png
Docs/Simulated_bin_mean_and_nonzero_proportion_288_noise0.png
Docs/tutorial.md
Example/README.md
LICENSE
NAMESPACE
R/ExtraFunctions.R
R/simATACCountClass.R
R/simATACEstimate.R
R/simATACFunctions.R
R/simATACSimulate.R
README.md
inst/extdata/GSE99172.txt
inst/extdata/hg19_genome_coordinates.txt
inst/extdata/hg38_genome_coordinates.txt
inst/extdata/mm10_genome_coordinates.txt
inst/extdata/mm9_genome_coordinates.txt
man/getBin.Rd
man/getBinNames.Rd
man/getCountFromSCE.Rd
man/getCountFromh5.Rd
man/getParameters.Rd
man/newsimATACCount.Rd
man/setDefautParameters.Rd
man/setParameters.Rd
man/simATACCompare.Rd
man/simATACCount.Rd
man/simATACEstBinMean.Rd
man/simATACEstLibSize.Rd
man/simATACEstNonZeroPro.Rd
man/simATACEstimate.Rd
man/simATACGenerate.Rd
man/simATACSimBinMean.Rd
man/simATACSimLibSize.Rd
man/simATACSimTrueCount.Rd
man/simATACSimZeroEntry.Rd
man/simATACSimulate.Rd
man/simATACget.Rd
man/simATACgetBinary.Rd
man/simATACgetFeatureByCell.Rd
man/simATACgetPeakByCell.Rd
man/simBinMeans.Rd
simATAC.Rproj
