├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── R ├── analysis.r ├── class_gene_bc_matrix.r ├── constants.r ├── data.r ├── help.r ├── io.r ├── normalize.r ├── plot.r └── util.r ├── README.md ├── data ├── gbm1.rda └── gbm2.rda ├── inst └── extdata │ ├── test_pipestance │ ├── lone_matrix.mtx │ └── outs │ │ ├── analysis │ │ ├── kmeans │ │ │ ├── 10_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 2_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 3_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 4_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 5_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 6_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 7_clusters │ │ │ │ └── clusters.csv │ │ │ ├── 8_clusters │ │ │ │ └── clusters.csv │ │ │ └── 9_clusters │ │ │ │ └── clusters.csv │ │ ├── pca │ │ │ └── projection.csv │ │ └── tsne │ │ │ └── projection.csv │ │ ├── filtered_gene_bc_matrices │ │ └── hg19 │ │ │ ├── barcodes.tsv │ │ │ ├── genes.tsv │ │ │ └── matrix.mtx │ │ └── metrics_summary.csv │ ├── test_pipestance_cr130 │ └── outs │ │ ├── analysis │ │ ├── clustering │ │ │ ├── graphclust │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_10_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_2_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_3_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_4_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_5_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_6_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_7_clusters │ │ │ │ └── clusters.csv │ │ │ ├── kmeans_8_clusters │ │ │ │ └── clusters.csv │ │ │ └── kmeans_9_clusters │ │ │ │ └── clusters.csv │ │ ├── diffexp │ │ │ ├── graphclust │ │ │ │ └── differential_expression.csv │ │ │ └── kmeans_2_clusters │ │ │ │ └── differential_expression.csv │ │ ├── pca │ │ │ └── 10_components │ │ │ │ ├── components.csv │ │ │ │ ├── dispersion.csv │ │ │ │ ├── genes_selected.csv │ │ │ │ ├── projection.csv │ │ │ │ └── variance.csv │ │ └── tsne │ │ │ └── 2_components │ │ │ └── projection.csv │ │ ├── filtered_gene_bc_matrices │ │ └── GRCh38 │ │ │ ├── barcodes.tsv │ │ │ ├── genes.tsv │ │ │ └── matrix.mtx │ │ ├── filtered_gene_bc_matrices_h5.h5 │ │ ├── metrics_summary.csv │ │ └── molecule_info.h5 │ ├── test_pipestance_h5 │ └── outs │ │ └── filtered_gene_bc_matrices_h5.h5 │ └── test_subsample │ └── outs │ ├── filtered_gene_bc_matrices │ └── hg19 │ │ ├── barcodes.tsv │ │ ├── genes.tsv │ │ └── matrix.mtx │ ├── metrics_summary.csv │ └── molecule_info.h5 ├── man ├── Arith-GeneBCMatrix-GeneBCMatrix-method.Rd ├── Arith-GeneBCMatrix-logical-method.Rd ├── Arith-GeneBCMatrix-numeric-method.Rd ├── Arith-logical-GeneBCMatrix-method.Rd ├── Arith-numeric-GeneBCMatrix-method.Rd ├── Compare-GeneBCMatrix-GeneBCMatrix-method.Rd ├── Compare-GeneBCMatrix-logical-method.Rd ├── Compare-GeneBCMatrix-numeric-method.Rd ├── Compare-logical-GeneBCMatrix-method.Rd ├── Compare-numeric-GeneBCMatrix-method.Rd ├── GeneBCMatrix-class.Rd ├── GeneBCMatrix-missing-method.Rd ├── Logic-GeneBCMatrix-GeneBCMatrix-method.Rd ├── Logic-GeneBCMatrix-logical-method.Rd ├── Logic-GeneBCMatrix-numeric-method.Rd ├── Logic-logical-GeneBCMatrix-method.Rd ├── Logic-numeric-GeneBCMatrix-method.Rd ├── Math-GeneBCMatrix-method.Rd ├── Math2-GeneBCMatrix-method.Rd ├── Summary-GeneBCMatrix-method.Rd ├── binary_op.Rd ├── binary_op_left.Rd ├── binary_op_right.Rd ├── bind-variables-to-fix-data.table-errors-when-packaging.Rd ├── cell_composition.Rd ├── cellrangerRkit.Rd ├── check_irlba.Rd ├── colMeans-GeneBCMatrix-method.Rd ├── colSums-GeneBCMatrix-method.Rd ├── compress_sequences.Rd ├── compute_sseq_params.Rd ├── concatenate_gene_bc_matrices.Rd ├── constants.Rd ├── csv_value_to_numeric.Rd ├── dim-GeneBCMatrix-method.Rd ├── dimnames-GeneBCMatrix-method.Rd ├── directory.exists.Rd ├── download_file_and_check.Rd ├── download_sample.Rd ├── equalize_gbms.Rd ├── format_barcode_string.Rd ├── gbm1.Rd ├── gbm2.Rd ├── gbm_pheatmap.Rd ├── get_barcode_sequence.Rd ├── get_clustering_path.Rd ├── get_correletion_scores.Rd ├── get_custom_col.Rd ├── get_gem_group.Rd ├── get_gene_dispersion.Rd ├── get_gene_index.Rd ├── get_genome_in_matrix_path.Rd ├── get_genomes_in_matrix_dir.Rd ├── get_matrix_dir_path.Rd ├── get_matrix_from_h5.Rd ├── get_matrix_path.Rd ├── get_mean_mapped_reads_per_cell.Rd ├── get_mean_raw_reads_per_cell.Rd ├── get_metric.Rd ├── get_nonzero_genes.Rd ├── get_ordered_gene_list_mean_diff.Rd ├── get_ordered_gene_list_sseq.Rd ├── get_ordered_gene_list_unique.Rd ├── get_pca_path.Rd ├── get_read_count_mtx.Rd ├── get_summary_csv_path.Rd ├── get_tsne_path.Rd ├── load_analysis_results_from_path.Rd ├── load_cellranger_analysis_results.Rd ├── load_cellranger_matrix.Rd ├── load_cellranger_matrix_from_files.Rd ├── load_cellranger_matrix_h5.Rd ├── load_cellranger_summary.Rd ├── load_molecule_info.Rd ├── load_molecule_info_from_path.Rd ├── log_gene_bc_matrix.Rd ├── merge_clusters.Rd ├── nb_exact_test.Rd ├── ncol-GeneBCMatrix-method.Rd ├── newGeneBCMatrix.Rd ├── normalize_barcode_sums_to_median.Rd ├── nrow-GeneBCMatrix-method.Rd ├── order_cell_by_clusters.Rd ├── plot_barcode_counts.Rd ├── plot_population_corr.Rd ├── plus-GeneBCMatrix-missing-method.Rd ├── prioritize_genes.Rd ├── prioritize_top_genes.Rd ├── rowMeans-GeneBCMatrix-method.Rd ├── rowSums-GeneBCMatrix-method.Rd ├── run_differential_expression.Rd ├── run_kmeans_clustering.Rd ├── run_pca.Rd ├── run_tsne.Rd ├── save_cellranger_matrix_h5.Rd ├── select_cells_by_clusterID.Rd ├── select_clusters_by_gene_markers.Rd ├── sparse_pca.Rd ├── sseq_differential_expression.Rd ├── subsample_gene_bc_matrix.Rd ├── train_multinomial.Rd ├── trunc_gbm_by_genes.Rd ├── unary_arith_op.Rd ├── unary_op.Rd ├── visualize_clusters.Rd ├── visualize_gene_markers.Rd ├── visualize_umi_counts.Rd ├── visualize_variable_genes.Rd └── write_cluster_specific_genes.Rd ├── scripts ├── download_samples.R ├── rkit-install-1.1.0.R ├── rkit-install-2.0.0.R ├── run_knitr.R └── saved_variables.R ├── tests ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── test_concat.r 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