Files in dleelab/iasvaExamples
iasva example data package
.DS_Store
.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
NAMESPACE
R/Darmanis_Brain_scRNAseq_Annotations.R
R/Darmanis_Brain_scRNAseq_Read_Counts.R
R/Lawlor_Islet_scRNAseq_Annotations.R
R/Lawlor_Islet_scRNAseq_Read_Counts.R
R/Patel_Glioblastoma_scRNAseq_Annotations.R
R/Patel_Glioblastoma_scRNAseq_Read_Counts.R
R/Xin_Islet_scRNAseq_Annotations.R
R/Xin_Islet_scRNAseq_Read_Counts.R
README.md
_workflowr.yml
analysis/.nojekyll
analysis/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd
analysis/_site.yml
analysis/detecting_hidden_heterogeneity.Rmd
analysis/hidden_heterogeneity_glioblastoma.Rmd
analysis/index.Rmd
analysis/license.Rmd
analysis/reviewer2_sim.Rmd
analysis/scRNASeq_simulation.Rmd
analysis/sim_study_KF_HF_genes_overlap.Rmd
analysis/tSNE_post_IA-SVA_3celltypes.Rmd
analysis/tSNE_post_IA-SVA_Xin_Islets.Rmd
code/README.md
data/.DS_Store
data/Darmanis_Brain_scRNAseq_Annotations.rda
data/Darmanis_Brain_scRNAseq_Read_Counts.rda
data/Lawlor_Islet_scRNAseq_Annotations.rda
data/Lawlor_Islet_scRNAseq_Read_Counts.rda
data/Patel_Glioblastoma_scRNAseq_Annotations.rda
data/Patel_Glioblastoma_scRNAseq_ENSG_ID.rda
data/Patel_Glioblastoma_scRNAseq_Read_Counts.rda
data/README.md
data/Xin_Islet_scRNAseq_Annotations.rda
data/Xin_Islet_scRNAseq_Read_Counts.rda
docs/.DS_Store
docs/.nojekyll
docs/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.html
docs/about.html
docs/detecting_hidden_heterogeneity.html
docs/figure/.DS_Store
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/geno_lib_size-1.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/plot_cor-1.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/plot_cor-2.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-1.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-10.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-11.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-2.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-3.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-4.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-5.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-6.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-7.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-8.png
docs/figure/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd/run_analyses-9.png
docs/figure/detecting_hidden_heterogeneity.Rmd/find_markers-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/normalization-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/num_detected_genes-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_iasva-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_iasva-2.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_iasva-3.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_iasva-4.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_pca-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_pca-2.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_sva-1.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_sva-2.png
docs/figure/detecting_hidden_heterogeneity.Rmd/run_tsne-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/find_markers_SV1-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/find_markers_SV1-2.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/gen_Figure3F-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/normalization-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/num_detected_genes-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/pca_plot-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/pca_plot-2.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_iasva-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_iasva-2.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_iasva-3.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_scran-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_sva-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_sva-2.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_tsne-1.png
docs/figure/hidden_heterogeneity_glioblastoma.Rmd/run_tsne_post_iasva-1.png
docs/figure/reviewer2_sim.Rmd/existing_methods-1.png
docs/figure/reviewer2_sim.Rmd/existing_methods-2.png
docs/figure/reviewer2_sim.Rmd/firstPC_residual-1.png
docs/figure/reviewer2_sim.Rmd/sim1-1.png
docs/figure/reviewer2_sim.Rmd/sim1-2.png
docs/figure/reviewer2_sim.Rmd/sim1-3.png
docs/figure/reviewer2_sim.Rmd/sim1-4.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected-1.png
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docs/figure/reviewer2_sim.Rmd/sim1_corrected-3.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected-4.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr-1.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr-2.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr-3.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr-4.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr-5.png
docs/figure/reviewer2_sim.Rmd/sim1_corrected_high_corr_extreme-1.png
docs/figure/reviewer2_sim.Rmd/sim2-1.png
docs/figure/reviewer2_sim.Rmd/sim2-2.png
docs/figure/reviewer2_sim.Rmd/sim_corrected_high_corr-1.png
docs/figure/reviewer2_sim.Rmd/sim_corrected_high_corr_challenging-1.png
docs/figure/scRNASeq_simulation.Rmd/hidden_factor_estimation-1.png
docs/figure/scRNASeq_simulation.Rmd/mean_var_relationship-1.png
docs/figure/scRNASeq_simulation.Rmd/simulate_data-1.png
docs/figure/scRNASeq_simulation.Rmd/simulate_data-2.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/assess_estimation_accuracy-1.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/comp_figures-1.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/iasva_hidden_factor_estimation-1.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/iasva_results_analysis-1.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/mean_var_relationship-1.png
docs/figure/sim_study_KF_HF_genes_overlap.Rmd/simulate_data-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/find_markers-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/find_markers_SV1_SV3-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/num_detected_genes-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_CellView-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_CellView-2.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_Seurat-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_Seurat-2.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_iasva-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_iasva-2.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_tsne-1.png
docs/figure/tSNE_post_IA-SVA_3celltypes.Rmd/run_tsne_post_iasva-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/corr_btw_SVs-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/find_markers_SV1-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/find_markers_SV3-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/load_data-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/load_data-2.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/num_detected_genes-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_CellView-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_CellView-2.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_Seurat-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_Seurat-2.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_Seurat-3.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_iasva-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_iasva-2.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_pca-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_sva-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_tsne-1.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_tsne-2.png
docs/figure/tSNE_post_IA-SVA_Xin_Islets.Rmd/run_tsne_post_iasva-1.png
docs/hidden_heterogeneity_glioblastoma.html
docs/index.html
docs/license.html
docs/reviewer2_sim.html
docs/scRNAseq_simulation.html
docs/sim_study_KF_HF_genes_overlap.html
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap.min.css
docs/site_libs/bootstrap-3.3.5/css/cerulean.min.css
docs/site_libs/bootstrap-3.3.5/css/cosmo.min.css
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docs/site_libs/bootstrap-3.3.5/css/simplex.min.css
docs/site_libs/bootstrap-3.3.5/css/spacelab.min.css
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docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
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docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
docs/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
docs/site_libs/bootstrap-3.3.5/js/bootstrap.js
docs/site_libs/bootstrap-3.3.5/js/bootstrap.min.js
docs/site_libs/bootstrap-3.3.5/js/npm.js
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docs/site_libs/highlightjs-9.12.0/highlight.js
docs/site_libs/highlightjs-9.12.0/textmate.css
docs/site_libs/jquery-1.11.3/jquery.min.js
docs/site_libs/navigation-1.1/codefolding.js
docs/site_libs/navigation-1.1/sourceembed.js
docs/site_libs/navigation-1.1/tabsets.js
docs/tSNE_post_IA-SVA_3celltypes.html
docs/tSNE_post_IA-SVA_Xin_Islets.html
iasvaExamples.Rproj
inst/.DS_Store
inst/doc/.DS_Store
inst/doc/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.html
inst/doc/detecting_hidden_heterogeneity.html
inst/doc/hidden_heterogeneity_glioblastoma.html
inst/doc/scRNAseq_simulation.html
inst/doc/sim_study_KF_HF_genes_overlap.html
inst/doc/tSNE_post_IA-SVA_3celltypes.html
inst/doc/tSNE_post_IA-SVA_Xin_Islets.html
man/Darmanis_Brain_scRNAseq_Annotations.Rd
man/Darmanis_Brain_scRNAseq_Read_Counts.Rd
man/Lawlor_Islet_scRNAseq_Annotations.Rd
man/Lawlor_Islet_scRNAseq_Read_Counts.Rd
man/Patel_Glioblastoma_scRNAseq_Annotations.Rd
man/Patel_Glioblastoma_scRNAseq_Read_Counts.Rd
man/Xin_Islet_scRNAseq_Annotations.Rd
man/Xin_Islet_scRNAseq_Read_Counts.Rd
output/.DS_Store
output/Brain_scRNASeq_neuron_astro_190_cells.pdf
output/Brain_scRNASeq_neuron_astro_190_cells_run_time.pdf
output/CC_genes.long.txt
output/CC_genes.short.txt
output/Clustering_analyses_figure2.pdf
output/Clustering_analyses_figure3_sv1.pdf
output/Clustering_analyses_figure4_Xin.pdf
output/Clustering_analyses_figure4_Xin_sv1.pdf
output/FigureL2.pdf
output/FigureS11_Xin_Islets_AllCells_IASVA_Markers_pheatmap.pdf
output/GeneOverlap.Fig1.pdf
output/GeneOverlap.Fig2.pdf
output/Lawlor_Islets_3Cells_CellView_Seurat_FigS.pdf
output/Lawlor_Islets_3Cells_IASVA_SV1SV3_rsqcutoff0.3_pheatmap_iasvaV0.95_Figure4_C.pdf
output/Lawlor_Islets_3Cells_IASVA_SV4_rsqcutoff0.3_pheatmap_iasvaV0.95.pdf
output/Lawlor_Islets_3Cells_IASVA_pairs4SVs_iasvaV0.95_black_FigS6.pdf
output/Lawlor_Islets_3Cells_IASVA_pairs4SVs_iasvaV0.95_color_FigS6.pdf
output/Lawlor_Islets_3Cells_SV1_SV3_Cell_Type_Genes_rsqcutoff0.3.txt
output/Lawlor_Islets_3Cells_SV4_Genes_rsqcutoff0.3.txt
output/Lawlor_Islets_3Cells_tSNE_IA-SVA_Fig4AB.pdf
output/Lawlor_Islets_Alpha_Doublets_Figure2_ABCD.pdf
output/Lawlor_Islets_Alpha_Doublets_SV2_Genes_rsqcutoff0.3.txt
output/Lawlor_Islets_Alpha_Doublets_SV2_Genes_rsqcutoff0.6.txt
output/Lawlor_Islets_Alpha_iasva_SV2Markers_rsqcutoff0.3_pheatmap_iasvaV0.95.pdf
output/Lawlor_Islets_Alpha_iasva_SV2Markers_rsqcutoff0.6_pheatmap_iasvaV0.95.pdf
output/Patel_Glioblastoma_MGH30_CellCycle_Figure3ABCD.pdf
output/Patel_Glioblastoma_MGH30_Cellcycle_SV1_Genes_rsqcutoff0.3.txt
output/Patel_Glioblastoma_MGH30_Cellcycle_SV1_Genes_rsqcutoff0.4.txt
output/Patel_Glioblastoma_MGH30_iasva_SV1_genes_rsqcutoff0.3_pheatmap_iasvaV0.95_Figure3F.pdf
output/README.md
output/Xin_Islets_AllCells_IASVA.pdf
output/Xin_Islets_AllCells_IASVA_nocolor.pdf
output/Xin_Islets_AllCells_PCA.pdf
output/Xin_Islets_AllCells_SV1_Genes_rsqcutoff0.2.txt
output/Xin_Islets_AllCells_SV1_Genes_rsqcutoff0.3.txt
output/Xin_Islets_AllCells_SV3_Genes_rsqcutoff0.2.txt
output/Xin_Islets_AllCells_SV3_Genes_rsqcutoff0.3.txt
output/Xin_Islets_AllCells_USVA.pdf
output/Xin_Islets_AllCells_tSNEByKnownFactors_FigureS9.pdf
output/Xin_Islets_All_demensionality_reduction_Figure4DEFG.pdf
output/absCor_gene_overlap_pct.pdf
output/gene_overlap.pdf
vignettes/.DS_Store
vignettes/Brain_scRNASeq_neuron_vs_oligodendrocyte_single_run.Rmd
vignettes/detecting_hidden_heterogeneity.Rmd
vignettes/hidden_heterogeneity_glioblastoma.Rmd
vignettes/scRNASeq_simulation.Rmd
vignettes/sim_study_KF_HF_genes_overlap.Rmd
vignettes/tSNE_post_IA-SVA_3celltypes.Rmd
vignettes/tSNE_post_IA-SVA_Xin_Islets.Rmd
