Files in elqumsan/RNAseqMVA
Application of Multivariate Analysis methods to RNA-seq Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.gitignore
R/DEG_computation.R
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/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/plot_filter_histogram.R
R/plotfigures.R
R/required_bioconductor.R
R/required_cran.R
R/select_projects_by_characteristics.R
R/stratified_sampling.R
R/study_case.R
R/summarize_error_tables.R
R/summarize_train_test_results.R
R/train_test_result.R
R/tune_classifiers.R
README.md
RNAseqMVA.Rproj
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
conda-rnaseqmva.yml
makefile
man/DEGordering.Rd
man/DataTableWithClasses.Rd
man/DataTableWithTrainTestSets.Rd
man/ErrorRateBoxPlot.Rd
man/ExtractPhenoTable.Rd
man/IterateTrainingTesting.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/StratifiedSampling.Rd
man/StudyCase.Rd
man/SummarizeErrorTable.Rd
man/SummarizeTrainTestResults.Rd
man/TrainTestResult.Rd
man/TuneClassifiers.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/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/plotKNNtuning.Rd
man/plotRFtuning.Rd
man/plotSVMtuning.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/01c_init_parallel_computing.R
misc/01d_reload_parameters.R
misc/02_load_and_normalise_counts.R
misc/02b_reload_counts.R
misc/05_tune_parameters.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/13_knn_impact_of_k.R
misc/14_svm_compare_results.R
misc/14_svm_impact_of_kernel.R
misc/14_svm_impact_of_parameters.R
misc/15_rf_impact_of_parameters.R
misc/main_processes.R
misc/obsolete/03_prcomp_computation.R
misc/obsolete/04_DEG_computation.R
misc/obsolete/05_variables_importance_computation.R
misc/obsolete/10_impact_of_normalisation.R
misc/obsolete/11_impact_of_normalization_and_Log2.R
misc/obsolete/12_visualization_prcomp_analysis.R
misc/obsolete/30_log2FC_computation.R
misc/protocol_loading_data_in_conventional_format.R
misc/recountIDS_with_problems.R
misc/recount_phenotable_bug.R
misc/recount_rx_bug.R
misc/summary_plots.R
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
srun_analysis.sh
srun_jobarray.mk
srun_jobarray.sh
vignettes/RNAseqMVA_user_guide.R
vignettes/RNAseqMVA_user_guide.Rmd
vignettes/RNAseqMVA_user_guide.html
vignettes/tutorial_RNAseqMVA_on_IFB-core-cluster.Rmd
vignettes/tutorial_RNAseqMVA_on_IFB-core-cluster.html
vignettes/vignettes
