Files in phillipnicol/pcDiffPop
Robust Identification of Perturbed Cell Types in Single-cell RNA-seq
.Rbuildignore
.gitignore
DESCRIPTION
Figures/augur_negative_control.R
Figures/count_deg/augur_increasing_samples.png
Figures/count_deg/count_deg.png
Figures/count_deg/count_deg_main.png
Figures/count_deg/count_deg_tree.png
Figures/count_deg/count_deg_updated.pdf
Figures/count_deg/count_deg_updated.png
Figures/count_deg/make.R
Figures/count_deg/make2.R
Figures/count_deg/muscat_scDist_runtime.png
Figures/count_deg/vary_sample_all_method.png
Figures/count_deg/zheng_full.pdf
Figures/scDist_negative_control.R
Figures/scDist_simulated.R
LICENSE
NAMESPACE
NEWS.md
R/condition_v_celltype_distance.R
R/featureImportance.R
R/plotting.R
R/scDist.R
R/simulateEffects.R
R/simulated_data.R
R/tree_analysis.R
R/zzz.R
README.Rmd
README.md
README_files/figure-gfm/unnamed-chunk-6-1.png
README_files/figure-gfm/unnamed-chunk-7-1.png
analysis/blish/code/.gitkeep
analysis/blish/code/blish.R
analysis/blish/data/.gitkeep
analysis/blish/data/celltype_v_condition.RDS
analysis/blish/data/scDist_results.RDS
analysis/blish/logs/.gitkeep
analysis/blish/plots/.gitkeep
analysis/blish/plots/blish_example.png
analysis/count_deg_blish/code/slurm_upsample.sh
analysis/count_deg_blish/code/slurm_upsample.sh~
analysis/count_deg_blish/code/upsample.R
analysis/count_deg_blish/data/.gitkeep
analysis/count_deg_blish/data/ct.size.RDS
analysis/count_deg_blish/data/cts.RDS
analysis/count_deg_blish/data/scDist_nDEG_TPR.png
analysis/count_deg_blish/data/upsample_res.RDS
analysis/count_deg_blish/data/upsample_time.RDS
analysis/count_deg_blish/logs/.gitkeep
analysis/count_deg_blish/plots/.gitkeep
analysis/count_deg_blish/plots/upsample_ct_path.png
analysis/count_deg_blish/plots/upsample_runtime.png
analysis/data/.gitkeep
analysis/negcontrol_blish/code/.gitkeep
analysis/negcontrol_blish/code/negcontrol.R
analysis/negcontrol_blish/code/slurm_negcontrol.sh
analysis/negcontrol_blish/code/slurm_negcontrol.sh~
analysis/negcontrol_blish/data/.gitkeep
analysis/negcontrol_blish/data/augur_results.RDS
analysis/negcontrol_blish/data/runtime.RDS
analysis/negcontrol_blish/data/scDist_pval_results.RDS
analysis/negcontrol_blish/data/scDist_pval_results_FMT.RDS
analysis/negcontrol_blish/data/scDist_results.RDS
analysis/negcontrol_blish/data/trabunzi_results.RDS
analysis/negcontrol_blish/logs/.gitkeep
analysis/negcontrol_blish/plots/.gitkeep
analysis/negcontrol_blish/plots/scDist_dist.png
analysis/negcontrol_blish/plots/scDist_pval.png
analysis/negcontrol_blish/plots/scDist_pval_FMT.png
analysis/negcontrol_blish/plots/trabunzi.png
analysis/negcontrol_sim/negcontrol_sim.R
analysis/sim_nct/code/num_ct.R
analysis/sim_nct/code/slurm_nct.sh
analysis/sim_nct/code/slurm_nct.sh~
analysis/sim_nct/code/slurm_nsamples.sh
analysis/sim_nct/code/slurm_nsamples.sh~
analysis/sim_nct/data/.gitkeep
analysis/sim_nct/data/sim_results.RDS
analysis/sim_nct/logs/.gitkeep
analysis/sim_nct/plots/.gitkeep
analysis/sim_samples/code/num_samples.R
analysis/sim_samples/code/slurm_nsamples.sh
analysis/sim_samples/code/slurm_nsamples.sh~
analysis/sim_samples/data/.gitkeep
analysis/sim_samples/data/sim_results.RDS
analysis/sim_samples/logs/.gitkeep
analysis/sim_samples/plots/.gitkeep
analysis/sim_samples/plots/many_samples_comparison.png
analysis/sim_samples/plots/many_samples_cor.png
analysis/sim_samples/plots/many_samples_rmse.png
analysis/tau_misspecified/code/.gitkeep
analysis/tau_misspecified/code/tau_misspecified.R
analysis/tau_misspecified/data/.gitkeep
analysis/tau_misspecified/data/tau_misspecified.RDS
analysis/tau_misspecified/logs/.gitkeep
analysis/tau_misspecified/plots/.gitkeep
analysis/tau_misspecified/plots/tau_misspecified.png
analysis/trabunzi2014/code/.gitkeep
analysis/trabunzi2014/data/.gitkeep
analysis/trabunzi2014/logs/.gitkeep
analysis/trabunzi2014/plots/.gitkeep
analysis/weighted_dist/code/weighted_dist.R
analysis/weighted_dist/data/.gitkeep
analysis/weighted_dist/data/sim_res.RDS
analysis/weighted_dist/logs/.gitkeep
analysis/weighted_dist/plots/.gitkeep
analysis/weighted_dist/plots/weighted_dist_sim.png
analysis/zheng_8eq/code/.gitkeep
analysis/zheng_8eq/code/cell_type_comp.R
analysis/zheng_8eq/code/cell_type_comp_equal.R
analysis/zheng_8eq/data/.gitkeep
analysis/zheng_8eq/data/cell.combos.dist.RDS
analysis/zheng_8eq/data/cell.combos.dist.equal.RDS
analysis/zheng_8eq/logs/.gitkeep
analysis/zheng_8eq/plots/.gitkeep
analysis/zheng_8eq/plots/blish_v_zheng_dist.png
analysis/zheng_8eq/plots/mds.png
man/DistPlot.Rd
man/FDRDistPlot.Rd
man/condition_v_celltype_distance.Rd
man/distGenes.Rd
man/plotBetas.Rd
man/scDist.Rd
man/scDist_tree.Rd
man/simData.Rd
scDist.Rproj
