Files in elqumsan/RNAseqMVA
Application of Multivariate Analysis methods to RNA-seq Data

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.gitignore
R/Data_table_with_classes.R R/Data_table_with_train_test_sets.R R/build_attribute.R R/deg_ordering.R R/error_rate_box_plot.R R/export_tables.R R/extract_pheno_table.R R/filter_data_table.R R/geochar_from_pheno.R R/hello.R R/init_parallel_computing.R R/init_recount_id.R R/iterate_training_testing.R R/libsize_barplot.R R/libsize_rank_plot.R R/load_counts.R R/load_recount_experiment.R R/load_required_bioconductor_packages.R R/load_required_cran_packages.R R/mainFunction.R R/memory_images.R R/merge_runs.R R/message_with_time.R R/misclassification_estimate.R R/normalize_count_table.R R/output_parameters.R R/plot_2pcs.R R/plotfigures.R R/required_bioconductor.R R/required_cran.R R/select_projects_by_characteristics.R R/study_case.R R/summarize_error_tables.R R/train_test_result.R README.md
RNAseqMVA.Rproj
Reports/.DS_Store
Rmd/.gitignore
Rmd/Recount_exploration.Rmd Rmd/pre-processing_summary_for_recount_datasets.Rmd
Rmd/pre-processing_summary_for_recount_datasets.html
Rmd/pre-processing_summary_for_recount_datasets.pdf
makefile
man/DEGordering.Rd man/DataTableWithClasses.Rd man/DataTableWithTrainTestSets.Rd man/ErrorRateBoxPlot.Rd man/ExtractPhenoTable.Rd man/IterateTrainingTesting.DataTableWithClasses.Rd man/IterateTrainingTesting.DataTableWithTrainTestSets.Rd man/IterateTrainingTesting.Rd man/IterateTrainingTesting.default.Rd man/LibsizeBarplot.Rd man/LibsizeRankPlot.Rd man/LoadRequiredBioconductorPackages.Rd man/LoadRequiredCRANPackages.Rd man/MergeRuns.Rd man/MisclassificationEstimate.Rd man/NormalizeSamples.Rd man/RunDESeq2.Rd man/RunDESeq2.StudyCase.Rd man/RunViRf.Rd man/RunViRf.StudyCase.Rd man/RunedgeR.Rd man/RunedgeR.StudyCase.Rd man/StudyCase.Rd man/SummarizeErrorTable.Rd man/TrainTestResult.Rd man/XYplot.Rd man/buildAttributes.DataTableWithClasses.Rd man/buildAttributes.DataTableWithTrainTestSets.Rd man/buildAttributes.Rd man/buildAttributes.default.Rd man/exportTables.DataTableWithClasses.Rd man/exportTables.DataTableWithTrainTestSets.Rd man/exportTables.Rd man/exportTables.StudyCase.Rd man/exportTables.default.Rd man/filterDataTable.Rd man/geocharFromPheno.Rd man/heatmap.TrainTestResult.Rd man/hello.Rd man/histCountsPerGeneClass.Rd man/histCountsPerGeneClass.StudyCase.Rd man/initParallelComputing.Rd man/initRecountID.Rd man/loadCounts.Rd man/loadMemoryImage.Rd man/loadRecountExperiment.Rd man/message.with.time.Rd man/outputParameters.Rd man/plot2PCs.Rd man/plotFigures.DataTableWithClasses.Rd man/plotFigures.Rd man/plotFilterHistograms.Rd man/print.DataTableWithClasses.Rd man/print.DataTableWithTrainTestSets.Rd man/print.StudyCase.Rd man/print.TrainTestResult.Rd man/saveMemoryImage.Rd man/selectProjectsByCharacteristics.Rd man/summary.DataTableWithClasses.Rd man/summary.DataTableWithTrainTestSets.Rd man/summary.StudyCase.Rd man/summary.default.Rd
misc/.gitignore
misc/00_project_parameters.yml
misc/01a_load_libraries.R misc/01b_load_parameters.R misc/02_load_and_normalise_counts.R misc/03_prcomp_computation.R misc/04_DEG_computation.R misc/05_variables_importance_computation.R misc/06_all_variables_vs_all_PCs.R misc/07_PCA_impact_of_PC_number.R misc/08_DEG_impact_of_top_gene_number.R misc/09_Importance_Variables_impact_of_top_genes.R misc/10_impact_of_normalisation.R misc/11_impact_of_normalization_and_Log2.R misc/12_visualization_prcomp_analysis.R
misc/13_knn_impact_of_parameters.R
misc/14_svm_impact_of_parameters.R misc/15_rf_impact_of_parameters.R misc/main_processes.R misc/protocol_loading_data_in_conventional_format.R misc/summary_plots.R
packrat/.DS_Store
packrat/lib/x86_64-apple-darwin13.4.0/3.3.2/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h
packrat/lib/x86_64-apple-darwin13.4.0/3.3.2/Rcpp/include/Rcpp/sugar/functions/cumsum.h
packrat/lib/x86_64-apple-darwin13.4.0/3.3.2/Rcpp/include/Rcpp/sugar/functions/diff.h
packrat/lib/x86_64-apple-darwin13.4.0/3.3.2/Rcpp/include/Rcpp/sugar/functions/duplicated.h
packrat/lib/x86_64-apple-darwin13.4.0/3.3.2/assertthat/help/paths.rds
elqumsan/RNAseqMVA documentation built on Aug. 21, 2018, 7:55 a.m.