Files in jokergoo/cola
Unsupervised subgroup classification based on consensus clustering

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.directory
R/00_S4_generic_methods.R R/00_classes.R R/cola.R R/collect.R R/consensus_partition.R R/correspond_rank.R R/david_dws.R R/get.R R/hierarchical_partition.R R/report.R R/run_all.R R/signatures.R R/stat.R R/test_with_known.R R/top_rows.R R/utils.R R/z.global.R README.md
Rprof.out
inst/extdata/.directory
inst/extdata/TCGA_GBM_microarray_subset.RData
inst/extdata/cola_hc_template.Rmd inst/extdata/cola_report_template.Rmd
inst/extdata/consensus_mat_list.RData
inst/extdata/custom.css
inst/extdata/example.rds
inst/extdata/jquery-1.12.4.js
inst/extdata/jquery-ui.css
inst/extdata/jquery-ui.js
inst/extdata/section_template.Rmd load.R man/AAC.rd man/ConsensusPartition-class.rd man/ConsensusPartitionList-class.rd man/Extract.ConsensusPartitionList.rd man/HierarchicalPartition-class.rd man/PAC.rd man/adjust_matrix.rd man/adjust_outlier.rd man/all_leaves-HierarchicalPartition-method.rd man/all_nodes-HierarchicalPartition-method.rd man/all_partition_methods.rd man/all_top_value_methods.rd man/cola.rd man/cola_report-ConsensusPartition-method.rd man/cola_report-ConsensusPartitionList-method.rd man/cola_report-HierarchicalPartition-method.rd man/cola_report-dispatch.rd man/collect_classes-ConsensusPartition-method.rd man/collect_classes-ConsensusPartitionList-method.rd man/collect_classes-HierarchicalPartition-method.rd man/collect_classes-dispatch.rd man/collect_plots-ConsensusPartition-method.rd man/collect_plots-ConsensusPartitionList-method.rd man/collect_plots-dispatch.rd man/consensus_heatmap-ConsensusPartition-method.rd man/consensus_partition.rd man/correspond_between_rankings.rd man/correspond_between_two_rankings.rd man/dimension_reduction-ConsensusPartition-method.rd man/dimension_reduction-HierarchicalPartition-method.rd man/dimension_reduction-dispatch.rd man/dimension_reduction-matrix-method.rd man/get_anno-ConsensusPartition-method.rd man/get_anno-ConsensusPartitionList-method.rd man/get_anno-dispatch.rd man/get_anno_col-ConsensusPartition-method.rd man/get_anno_col-ConsensusPartitionList-method.rd man/get_anno_col-dispatch.rd man/get_best_k-ConsensusPartition-method.rd man/get_best_k-ConsensusPartitionList-method.rd man/get_best_k-dispatch.rd man/get_class-ConsensusPartition-method.rd man/get_class-ConsensusPartitionList-method.rd man/get_class-HierarchicalPartition-method.rd man/get_class-dispatch.rd man/get_classes-ConsensusPartition-method.rd man/get_classes-ConsensusPartitionList-method.rd man/get_classes-HierarchicalPartition-method.rd man/get_classes-dispatch.rd man/get_consensus-ConsensusPartition-method.rd man/get_matrix-ConsensusPartition-method.rd man/get_matrix-ConsensusPartitionList-method.rd man/get_matrix-dispatch.rd man/get_membership-ConsensusPartition-method.rd man/get_param-ConsensusPartition-method.rd man/get_signatures-ConsensusPartition-method.rd man/get_signatures-HierarchicalPartition-method.rd man/get_signatures-dispatch.rd man/get_single_run-ConsensusPartitionList-method.rd man/get_single_run-HierarchicalPartition-method.rd man/get_single_run-dispatch.rd man/get_stat-ConsensusPartition-method.rd man/get_stat-ConsensusPartitionList-method.rd man/get_stat-dispatch.rd man/guess_best_k-ConsensusPartition-method.rd man/guess_best_k-ConsensusPartitionList-method.rd man/guess_best_k-dispatch.rd man/hierarchical_partition.rd man/knitr_add_tab_item.rd man/knitr_insert_tabs.rd man/max_depth-HierarchicalPartition-method.rd man/membership_heatmap-ConsensusPartition-method.rd man/plot_ecdf-ConsensusPartition-method.rd man/reduce_david_results.rd man/register_partition_fun.rd man/register_partition_method.rd man/register_top_value_fun.rd man/register_top_value_method.rd man/remove_partition_method.rd man/remove_top_value_method.rd man/run_all_consensus_partition_methods.rd man/select_partition_number-ConsensusPartition-method.rd man/show-ConsensusPartition-method.rd man/show-ConsensusPartitionList-method.rd man/show-HierarchicalPartition-method.rd man/show-dispatch.rd man/signature_density-ConsensusPartition-method.rd man/submit_to_david.rd man/test_between_factors.rd man/test_to_known_factors-ConsensusPartition-method.rd man/test_to_known_factors-ConsensusPartitionList-method.rd man/test_to_known_factors-HierarchicalPartition-method.rd man/test_to_known_factors-dispatch.rd man/top_rows_heatmap-ConsensusPartitionList-method.rd man/top_rows_heatmap-dispatch.rd man/top_rows_heatmap-matrix-method.rd man/top_rows_overlap-ConsensusPartitionList-method.rd man/top_rows_overlap-dispatch.rd man/top_rows_overlap-list-method.rd man/top_rows_overlap-matrix-method.rd man/venn_euler.rd run_all_jobs.R
test_not_run/.directory
test_not_run/download_TCGA.R test_not_run/generate_plots.R test_not_run/hipo15_subgroup.R test_not_run/hipo15_subgroups_deseq2.R test_not_run/signatue_density.R test_not_run/test_10X.R test_not_run/test_AUC.R test_not_run/test_asthma.R test_not_run/test_asthma_dkfz.R test_not_run/test_gbm_methylation.R test_not_run/test_gbm_scrnaseq.R test_not_run/test_hipo16_rnaseq.R test_not_run/test_hipo43.R test_not_run/test_hipo50.R test_not_run/test_recount.R test_not_run/test_scrnaseq.R test_not_run/test_tcga_cohorts.R test_not_run/test_tcga_gbm.R test_not_run/test_tcga_paad.R test_not_run/test_tcga_subset.R vignettes_not_run/AAC.R vignettes_not_run/PAC.R vignettes_not_run/TCGA_gbm_microarray_subgroups.Rmd
vignettes_not_run/consensus_partition_framework.png
vignettes_not_run/custom.css
vignettes_not_run/silhouette.R
jokergoo/cola documentation built on April 20, 2018, 4:14 p.m.