├── LICENSE ├── Machine Learning └── randomForest.R ├── README.md ├── _config.yml ├── clustering ├── bin │ └── kmeans.R ├── how_to_run ├── input │ ├── example.FS │ ├── example.mx │ └── input_file_format └── output │ ├── example.kmeans.3.mx │ ├── example.kmeans.3.pdf │ ├── example.kmeans.4.mx │ └── example.kmeans.4.pdf ├── feature_selection ├── bin │ ├── Delete_SBS_combine.R │ ├── Delete_by_rank_combine.R │ ├── cv.IMP.R │ ├── cv.idx.R │ ├── cv.test.R │ └── lasso.R ├── how_to_run_lasso ├── how_to_run_wrapper_step0 ├── how_to_run_wrapper_step1_IMP ├── how_to_run_wrapper_step1_IMP_SBS ├── input │ ├── example.initial.FS │ ├── example.train.mx │ └── input_file_format ├── output │ ├── example.selected.FS.IMP │ ├── example.selected.FS.IMP_SBS │ └── example.selected.FS.lasso └── tmp │ ├── IMP │ ├── delete │ │ ├── feat │ │ │ ├── feat.0 │ │ │ ├── feat.1 │ │ │ ├── feat.10 │ │ │ ├── feat.11 │ │ │ ├── feat.12 │ │ │ ├── feat.13 │ │ │ ├── feat.14 │ │ │ ├── feat.15 │ │ │ ├── feat.16 │ │ │ ├── feat.17 │ │ │ ├── feat.18 │ │ │ ├── feat.19 │ │ │ ├── feat.2 │ │ │ ├── feat.20 │ │ │ ├── feat.21 │ │ │ ├── feat.22 │ │ │ ├── feat.3 │ │ │ ├── feat.4 │ │ │ ├── feat.5 │ │ │ ├── feat.6 │ │ │ ├── feat.7 │ │ │ ├── feat.8 │ │ │ └── feat.9 │ │ ├── haha.R │ │ ├── haha.Rout │ │ ├── log │ │ │ ├── log_del.0 │ │ │ ├── log_del.1 │ │ │ ├── log_del.10 │ │ │ ├── log_del.11 │ │ │ ├── log_del.12 │ │ │ ├── log_del.13 │ │ │ ├── log_del.14 │ │ │ ├── log_del.15 │ │ │ ├── log_del.16 │ │ │ ├── log_del.17 │ │ │ ├── log_del.18 │ │ │ ├── log_del.19 │ │ │ ├── log_del.2 │ │ │ ├── log_del.20 │ │ │ ├── log_del.21 │ │ │ ├── log_del.22 │ │ │ ├── log_del.3 │ │ │ ├── log_del.4 │ │ │ ├── log_del.5 │ │ │ ├── log_del.6 │ │ │ ├── log_del.7 │ │ │ ├── log_del.8 │ │ │ └── log_del.9 │ │ ├── perf │ │ │ ├── perf_del.0 │ │ │ ├── perf_del.1 │ │ │ ├── perf_del.10 │ │ │ ├── perf_del.11 │ │ │ ├── perf_del.12 │ │ │ ├── perf_del.13 │ │ │ ├── perf_del.14 │ │ │ ├── perf_del.15 │ │ │ ├── perf_del.16 │ │ │ ├── perf_del.17 │ │ │ ├── perf_del.18 │ │ │ ├── perf_del.19 │ │ │ ├── perf_del.2 │ │ │ ├── perf_del.20 │ │ │ ├── perf_del.21 │ │ │ ├── perf_del.22 │ │ │ ├── perf_del.3 │ │ │ ├── perf_del.4 │ │ │ ├── perf_del.5 │ │ │ ├── perf_del.6 │ │ │ ├── perf_del.7 │ │ │ ├── perf_del.8 │ │ │ └── perf_del.9 │ │ ├── perf_del_sum.pdf │ │ ├── perf_del_sum.txt │ │ └── qsub │ │ │ ├── qsub_del.0 │ │ │ ├── qsub_del.1 │ │ │ ├── qsub_del.10 │ │ │ ├── qsub_del.11 │ │ │ ├── qsub_del.12 │ │ │ ├── qsub_del.13 │ │ │ ├── qsub_del.14 │ │ │ ├── qsub_del.15 │ │ │ ├── qsub_del.16 │ │ │ ├── qsub_del.17 │ │ │ ├── qsub_del.18 │ │ │ ├── qsub_del.19 │ │ │ ├── qsub_del.2 │ │ │ ├── qsub_del.20 │ │ │ ├── qsub_del.21 │ │ │ ├── qsub_del.22 │ │ │ ├── qsub_del.3 │ │ │ ├── qsub_del.4 │ │ │ ├── qsub_del.5 │ │ │ ├── qsub_del.6 │ │ │ ├── qsub_del.7 │ │ │ ├── qsub_del.8 │ │ │ └── qsub_del.9 │ └── rank │ │ ├── IMP │ │ └── rank │ ├── IMP_SBS │ └── delete │ │ ├── feat │ │ ├── baseF.0 │ │ ├── baseF.1.1 │ │ ├── baseF.1.2 │ │ ├── baseF.1.3 │ │ ├── baseF.1.4 │ │ ├── baseF.1.5 │ │ ├── baseF.1.6 │ │ ├── baseF.1.7 │ │ ├── baseF.2.1 │ │ ├── baseF.2.2 │ │ ├── baseF.2.4 │ │ ├── baseF.2.5 │ │ ├── baseF.2.6 │ │ ├── baseF.2.7 │ │ ├── baseF.3.1 │ │ ├── baseF.3.2 │ │ ├── baseF.3.4 │ │ ├── baseF.3.6 │ │ ├── baseF.3.7 │ │ ├── baseF.4.1 │ │ ├── baseF.4.2 │ │ ├── baseF.4.4 │ │ ├── baseF.4.7 │ │ ├── baseF.5.1 │ │ ├── baseF.5.2 │ │ ├── baseF.5.4 │ │ └── delF.0 │ │ ├── foo1 │ │ ├── foo2 │ │ ├── foo3 │ │ ├── foo4 │ │ ├── foo5 │ │ ├── haha.R │ │ ├── haha.Rout │ │ ├── log │ │ ├── log_del.0 │ │ ├── log_del.1.1 │ │ ├── log_del.1.2 │ │ ├── log_del.1.3 │ │ ├── log_del.1.4 │ │ ├── log_del.1.5 │ │ ├── log_del.1.6 │ │ ├── log_del.1.7 │ │ ├── log_del.2.1 │ │ ├── log_del.2.2 │ │ ├── log_del.2.4 │ │ ├── log_del.2.5 │ │ ├── log_del.2.6 │ │ ├── log_del.2.7 │ │ ├── log_del.3.1 │ │ ├── log_del.3.2 │ │ ├── log_del.3.4 │ │ ├── log_del.3.6 │ │ ├── log_del.3.7 │ │ ├── log_del.4.1 │ │ ├── log_del.4.2 │ │ ├── log_del.4.4 │ │ ├── log_del.4.7 │ │ ├── log_del.5.1 │ │ ├── log_del.5.2 │ │ └── log_del.5.4 │ │ ├── perf │ │ ├── perf_del.0 │ │ ├── perf_del.1.1 │ │ ├── perf_del.1.2 │ │ ├── perf_del.1.3 │ │ ├── perf_del.1.4 │ │ ├── perf_del.1.5 │ │ ├── perf_del.1.6 │ │ ├── perf_del.1.7 │ │ ├── perf_del.2.1 │ │ ├── perf_del.2.2 │ │ ├── perf_del.2.4 │ │ ├── perf_del.2.5 │ │ ├── perf_del.2.6 │ │ ├── perf_del.2.7 │ │ ├── perf_del.3.1 │ │ ├── perf_del.3.2 │ │ ├── perf_del.3.4 │ │ ├── perf_del.3.6 │ │ ├── perf_del.3.7 │ │ ├── perf_del.4.1 │ │ ├── perf_del.4.2 │ │ ├── perf_del.4.4 │ │ ├── perf_del.4.7 │ │ ├── perf_del.5.1 │ │ ├── perf_del.5.2 │ │ └── perf_del.5.4 │ │ ├── qsub │ │ ├── qsub_del.0 │ │ ├── qsub_del.1.1 │ │ ├── qsub_del.1.2 │ │ ├── qsub_del.1.3 │ │ ├── qsub_del.1.4 │ │ ├── qsub_del.1.5 │ │ ├── qsub_del.1.6 │ │ ├── qsub_del.1.7 │ │ ├── qsub_del.2.1 │ │ ├── qsub_del.2.2 │ │ ├── qsub_del.2.4 │ │ ├── qsub_del.2.5 │ │ ├── qsub_del.2.6 │ │ ├── qsub_del.2.7 │ │ ├── qsub_del.3.1 │ │ ├── qsub_del.3.2 │ │ ├── qsub_del.3.4 │ │ ├── qsub_del.3.6 │ │ ├── qsub_del.3.7 │ │ ├── qsub_del.4.1 │ │ ├── qsub_del.4.2 │ │ ├── qsub_del.4.4 │ │ ├── qsub_del.4.7 │ │ ├── qsub_del.5.1 │ │ ├── qsub_del.5.2 │ │ └── qsub_del.5.4 │ │ └── summary │ │ ├── bestFeat │ │ └── bestPerf │ └── idx │ └── cv.idx ├── plots ├── 1.boxplots.R ├── 10.ballonplots.R ├── 11.vennpieplots.R ├── 2.violinplots.R ├── 3.histogramplots.R ├── 4.densityplots.R ├── 5.dotplots.R ├── 6.scatterplots.R ├── 7.volcanoplots.R ├── 8.manhattanplots.R ├── 9.heatmaps.R ├── README.md ├── ballon_plots_GO.txt ├── box_plots_mtcars.txt ├── heatmaps.txt ├── histogram_plots.txt ├── manhattan_plots_gwasResults.txt └── volcano_plots.txt └── pre-processGff ├── bin ├── getlncRNAexon.py ├── makeIntron.py ├── specify5-3UTR.R └── specify5-3UTR.py ├── output └── clean_gtf │ ├── 3prime_overlapping_ncrna.gtf │ ├── Mt_rRNA.gtf │ ├── Mt_tRNA.gtf │ ├── antisense.gtf │ ├── lincRNA.gtf │ ├── miRNA.gtf │ ├── misc_RNA.gtf │ ├── non_coding.gtf │ ├── rRNA.gtf │ ├── sense_intronic.gtf │ ├── sense_overlapping.gtf │ ├── snRNA.gtf │ └── snoRNA.gtf ├── 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-------------------------------------------------------------------------------- 1 | 0.923527190332326 2 | 69 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.1: -------------------------------------------------------------------------------- 1 | 0.925793051359517 2 | 66 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.10: -------------------------------------------------------------------------------- 1 | 0.926925981873112 2 | 39 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.11: -------------------------------------------------------------------------------- 1 | 0.926359516616314 2 | 36 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.12: -------------------------------------------------------------------------------- 1 | 0.925981873111782 2 | 33 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.13: -------------------------------------------------------------------------------- 1 | 0.925415407854985 2 | 30 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.14: -------------------------------------------------------------------------------- 1 | 0.924848942598187 2 | 27 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.15: -------------------------------------------------------------------------------- 1 | 0.923904833836858 2 | 24 3 | -------------------------------------------------------------------------------- /feature_selection/tmp/IMP/delete/perf/perf_del.16: 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