Files in jakeyeung/scchic-functions

R/AnnotationFunctions.R R/ArrowFunctions.R R/Aux.R R/AuxB6.R R/AuxLDA.R R/BatchEffectFunctions.R R/BedFunctions.R R/ClusteringFunctions.R R/DistFuncs.R R/DoubleStaining.R R/EntropyFunctions.R R/FitFunctions.R R/FitFunctionsDownstream.R R/GeneListFunctions.R R/GenesetFunctions.R R/GlmFunctions.R R/HandleCSVs.R R/IntegrateData.R R/LSI.R R/MaraDownstream.R R/Math.R R/MatrixFunctions.R R/MixtureModelFunctions.R R/MultinomFunctions.R R/ParseStrings.R R/PlateLayoutFunctions.R R/PlateLayoutFunctions2.R R/PlotFunctions.R R/PublicDataFuncs.R R/QCFunctionsGastru.R R/SpikeInFunctions.R R/VariabilityFunctions.R R/hello.R R/ridgeInR.R README.md man/hello.Rd scripts/Rfunctions.DontUse/AnnotationFunctions.R scripts/Rfunctions.DontUse/Aux.R scripts/Rfunctions.DontUse/AuxB6.R scripts/Rfunctions.DontUse/AuxLDA.R scripts/Rfunctions.DontUse/DoubleStaining.R scripts/Rfunctions.DontUse/FitFunctions.R scripts/Rfunctions.DontUse/LSI.R scripts/Rfunctions.DontUse/Math.R scripts/Rfunctions.DontUse/ParseStrings.R scripts/Rfunctions.DontUse/PlotFunctions.R scripts/Rfunctions.DontUse/QCFunctionsGastru.R scripts/Rfunctions.DontUse/Rfunctions.oldDontUse/AuxLDA.R scripts/Rfunctions.DontUse/Rfunctions.oldDontUse/QCFunctionsGastru.R scripts/Rfunctions.DontUse/VariabilityFunctions.R scripts/Rfunctions.DontUse/ZebrafishFunctions.R scripts/Rfunctions.DontUse/hello.R scripts/memux_scripts/make_clusters_from_LDA_outputs.R scripts/memux_scripts/make_clusters_from_LDA_outputs.UseClusterColname.R scripts/memux_scripts/make_clusters_from_csv.R scripts/memux_scripts/make_clusters_from_topics_mixturemodel.R scripts/memux_scripts/setup_objs_for_unmixing_topics_general.R scripts/memux_scripts/unmixing_downstream_split_reads_script.R scripts/memux_scripts/unmixing_downstream_split_reads_script.UnevenRows.R scripts/memux_scripts/unmixing_downstream_split_reads_script.UseClusterColname.R scripts/motevo_scripts/lib/annotate_bed_to_gene_and_distance.R scripts/motevo_scripts/lib/annotate_bed_to_gene_and_distance.Zebrafish.R scripts/motevo_scripts/lib/annotate_distance_on_bed.R scripts/motevo_scripts/lib/bed_to_sql.R scripts/motevo_scripts/lib/lda_to_norm_mat.R scripts/motevo_scripts/lib/make_sitecount_matrix.R scripts/motevo_scripts/lib/make_sitecount_matrix_from_bed.R scripts/motevo_scripts/lib/pwm_to_seqlogo.R scripts/motevo_scripts/lib/run_ridge_regression2.R scripts/processing_scripts/choose_k_LDA_output.R scripts/processing_scripts/convert_txt_to_rds_count_table.R scripts/processing_scripts/csv_to_RData_TSS.R scripts/processing_scripts/filter_cells_by_totalcuts_TAfrac_intrachromovar.R scripts/processing_scripts/filter_good_cells_by_cellfile.R scripts/processing_scripts/filter_good_cells_good_bins.R scripts/processing_scripts/glmpca_with_spikeins.R scripts/processing_scripts/load_objs_run_fits.R scripts/processing_scripts/make_merged_exprs_mat_for_MARA.R scripts/processing_scripts/make_merged_exprs_mat_for_MARA.args.R scripts/processing_scripts/make_merged_exprs_mat_from_GLMPCA_for_MARA.args.R scripts/processing_scripts/mat_to_sparse_mat_new_slidewin_format.R scripts/processing_scripts/mat_to_sparse_mat_new_slidewin_format.tempdir.R scripts/processing_scripts/mat_to_sparse_mat_new_slidewin_format_allele.R scripts/processing_scripts/mat_to_sparse_mat_tss_format.R scripts/processing_scripts/plot_LDA_topics.R scripts/processing_scripts/project_new_samples_on_LDA.old.R scripts/processing_scripts/project_new_samples_on_LDA_bin.R scripts/processing_scripts/run_GLMPCA_with_LDA_init.R scripts/processing_scripts/run_GLMPCA_with_LDA_init_spikeins_plate.R scripts/processing_scripts/run_GLMPCA_with_LDA_init_spikeins_plate.from_imputed.R scripts/processing_scripts/run_GLMPCA_with_LDA_init_spikeins_plate.from_project.R scripts/processing_scripts/run_LDA_model.R scripts/processing_scripts/run_LDA_model2.R scripts/processing_scripts/run_LDA_model3.R scripts/processing_scripts/run_fastTopics.R scripts/processing_scripts/run_hidden_domains.R scripts/processing_scripts/sparse_mat_to_mm.R scripts/ridge_scripts/ridgeInR.R scripts/ridge_scripts/run_ridge_regression2.R