Files in jakeyeung/SleepDepAnalysis
Statistical Model and Data For Analyzing RNAseq Sleep Deprivation Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AtacSeqFunctions.R
R/BiomartFunctionsSleep.R
R/ClusteringFunctions.R
R/DatabaseFunctions.R
R/DoTtest.R
R/EegFunctions.R
R/EnvironmentsFunctions.R
R/FitFunctions.R
R/FitFunctions_Downstream.R
R/GetClockGenes.R
R/GetSwitchHash.R
R/GetTFs.R
R/HandleRawDataFunctions.R
R/HashFunctions.R
R/IntegerFunctions.R
R/LoadData.R
R/MaraDownstream.R
R/MdlNames.R
R/MergingAssigningSamples.R
R/ModelSelectionFunctions.R
R/PhaseFunctions.R
R/PlotEnrichment.R
R/PlotFun_Maxime.R
R/PlotFunctions.R
R/PlotFunctions.auxiliary.R
R/PlotGeneTimeCourse.R
R/PlotMotifTimeCourse.R
R/README_stuff/README.R
R/README_stuff/README_files/figure-markdown_strict/unnamed-chunk-2-1.png
R/README_stuff/README_files/figure-markdown_strict/unnamed-chunk-3-1.png
R/README_stuff/plot_genelists.R
R/RnaSeqFunctions.R
R/RoundTwoPCAScripts.R
R/SleuthFunctions.R
R/SmoothingFunctions.R
R/StringFunctions.R
R/SummarizeModels.R
R/TimeShiftFunctions.R
R/WellingtonFunctions.R
R/data.R
README.R
README.md
README_files/figure-markdown_strict/unnamed-chunk-2-1.png
README_files/figure-markdown_strict/unnamed-chunk-3-1.png
README_files/figure-markdown_strict/unnamed-chunk-6-1.png
data/dat.long.cleaned.techmerged_zt24assigned.RData
data/dat.long.kallisto.combat.mean_only.FALSE.exprs_cutoff.2.5.RData
data/fits_Rcpp_bugfix.maxiter.2000.LogLBicCorrected.model.sleep_mix_mixedaf_ampfreestep.lambda.1000.dolinear.FALSE.minhl.0.33.RData
data/fits_Rcpp_sleuthfilt.maxiter.3000.model.LogLBicCorrected.model.sleep_mix_mixedaf.lambda.1000.dolinear.FALSE.minhl.0.33.RData
data/kmeans_objs.RData
data/motifs_and_TFs.list
data/sleep_deprivation_gene_exprs_all/Activities
data/sleep_deprivation_gene_exprs_all/Colnames
data/sleep_deprivation_gene_exprs_all/FOV
data/sleep_deprivation_gene_exprs_all/Lambda
data/sleep_deprivation_gene_exprs_all/StandardError
data/sleep_deprivation_gene_exprs_all/Zscores
data/sleep_deprivation_gene_exprs_all/r.Robj
data/tables/affymetrix_table/GPL1261-56135.txt
data/tables/dat_exprs_clstr_model.txt
data/tables/dat_scaledexprs_clstr_model.txt
data/tables/model_selection_output_multieeg.txt
data/tables/parameter_estimates_from_fit/parameter_estimates_from_fit_sleep_genes.txt
data/tables/rhyth_go_terms.txt
data/tables/rhythmic_genes_brain/brain_rhythmic_genes.tar.gz
data/tables/rhythmic_genes_brain/tiss_BS.pdf
data/tables/rhythmic_genes_brain/tiss_BS.txt
data/tables/rhythmic_genes_brain/tiss_Cere.pdf
data/tables/rhythmic_genes_brain/tiss_Cere.txt
data/tables/rhythmic_genes_brain/tiss_Hypo.pdf
data/tables/rhythmic_genes_brain/tiss_Hypo.txt
data/tables/tables_atac_rnaseq_correlation/atac_gene_cor.txt
data/tables/tables_for_charlotte.2018-08-13/dat_sd_ttest_model_cluster.txt
data/tables/tables_for_charlotte.2018-08-14/dat_sd_ttest_model_cluster.txt
data/tables/tables_for_charlotte.2018-08-16/fit.rhyth.base.annot.txt
data/tables/tables_from_franken.2018-09-04/78genes_Mongrain2010.txt
data/tables/tables_from_franken.2018-09-04/Maret_Table_3_2032_rhythmic_under_baseline.xlsx
data/tables/tables_from_franken.2018-09-04/Maret_Table_4_391_still_circadian_after_4_SDs.xlsx
data/tables/tables_from_franken.2018-09-04/Maret_Table_5_343_affected_by_SD_independent_of_time-of-day.xlsx
data/wake.df.method.mode.RData
interactive_scripts/explore_param_of_fits.R
man/hello.Rd
