Files in MyersGroup/testisAtlas

testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq

R/functions_enrichment.R R/functions_ordering.R R/functions_single_cell.R R/functions_tss.R README.md analysis/10_merge-DGEs.Rmd analysis/11_QC.Rmd analysis/12_update-dimnames.Rmd analysis/20_SDA-component-number.Rmd analysis/21_SDA-random-seed.Rmd analysis/22_SDA-WT.Rmd analysis/23.5_tSNE-Umap.Rmd analysis/23.6_Somatic_Cells.Rmd analysis/23_SDA.Rmd analysis/24_Gene-annotations.Rmd analysis/25_iRegulon-enrichment.Rmd analysis/26_GO-enrichment.Rmd analysis/27_Meiotic-components.Rmd analysis/28_Somatic-components.Rmd analysis/29.5_odd_component_48_diff_expression.Rmd analysis/29_Other-Components.Rmd analysis/30.5_Transcription_programme_cartoon.Rmd analysis/30_Pseudotime.Rmd analysis/31_MSCI.Rmd analysis/32_Meiotic-gene-families.Rmd analysis/33_matched-differential-expression.Rmd analysis/34.5_Other_Factorisations.Rmd analysis/34_Imputation-evaluation.Rmd analysis/35_Alzheimers.Rmd analysis/36_MCA.Rmd analysis/40_MotifFinder-ranking.Rmd analysis/41_Denovo-motifFinder-systematic.Rmd analysis/42.5_ChIPseq_reanalysis.Rmd analysis/42_Denovo-TF-overview.Rmd analysis/51_figure-creation.Rmd analysis/52_Animation.Rmd man/GO_enrichment.Rd man/Mode.Rd man/binned_mean_regprob.Rd man/clustered_heatmap.Rd man/compare_factorisations.Rd man/component_enrichment.Rd man/correlate_regprobs.Rd man/create_grob_list.Rd man/dmultinom_v.Rd man/download_flank_sequences.Rd man/download_tss.Rd man/export_FASTA.Rd man/export_all_pwms.Rd man/expression_dt.Rd man/find_motifs_parallel.Rd man/gene_expression_pseudotime.Rd man/gene_list.Rd man/get_component_motifs.Rd man/get_density.Rd man/get_top_genes.Rd man/go_volcano_plot.Rd man/imputed_vs_raw.Rd man/load2.Rd man/load_component_orderings.Rd man/load_curve_data.Rd man/log_colour_scale.Rd man/manhatten_plot.Rd man/match_cells2.Rd man/mean_prob_bycomp.Rd man/melt_genes.Rd man/motif_consensus.Rd man/plotCellAUC.Rd man/plot_cell_scores.Rd man/plot_component_regprobs.Rd man/plot_meanprob_bycomp.Rd man/plot_motif_matches.Rd man/plot_pseudotime_expression_panel.Rd man/princurve_bootstrap.Rd man/print_loadings_scores.Rd man/print_pca.Rd man/print_raw_tsne.Rd man/print_tsne.Rd man/ptorder.Rd man/reverse_normalisation.Rd man/rotate_SDA.Rd man/rotate_matrix.Rd man/rotate_tsne.Rd man/save2.Rd man/sda_predict.Rd man/sequence_matrix.Rd man/single_component_enrichment.Rd man/sort_matrix.Rd man/split_loadings.Rd man/ternaryColours.Rd man/tricolour_tsne.Rd shinyApp/README.md shinyApp/app.R shinyApp/setup_low_memory_mode.R vignettes/vignette.Rmd vignettes/vignette.md