Files in Benjamin-Vincent-Lab/binfotron

Binfotron Bioinformatics Analysis Tools Suite

R/binfotron.R R/calc_fdr.R R/calc_impres.R R/convert_genes.R R/data_navigation.R R/differential_expression.R R/diversity_fxns.R R/encoding_decoding.R R/extract_mixcr_analyze_shotgun_reports.R R/find_central_clone.R R/find_low_variance_clms.R R/find_similar_clms.R R/general_utilities.R R/housekeeping_annotation.R R/import_model_data_et_al.R R/plot_cumulative_features.R R/plot_error_volcano.R R/plot_waterfall.R R/regression.R R/stackable_functions.R R/stacks.R R/view_boxplot.R R/view_clustered_myHeatmap.R R/view_volcano_plot.R README.md inst/models/subsampled_stig_2-4096_model/RNASeq_subsampled_random_abundance_TRB_100cv_10alpha.pdf inst/models/subsampled_stig_4097-65536_model/RNASeq_subsampled_random_abundance_TRB_100cv_10alpha.pdf inst/models/tcga_ab1025-65K_ent1-8/tcga_distribution_100cv_10alpha.pdf inst/models/tcga_ab8-1024_ent1-8/tcga_distribution_100cv_10alpha.pdf man/add_comments.Rd man/add_filler.Rd man/announce_end_of_stack.Rd man/announce_start_of_stack.Rd man/announce_total_time.Rd man/as.bullet.Rd man/as.footer.Rd man/as.header1.Rd man/as.header2.Rd man/balanced_folds.Rd man/bgv_lab_prep_count_data_for_deseq2.Rd man/bgv_lab_prep_count_data_for_gene_signature.Rd man/binfotron-package.Rd man/break_sentence.Rd man/calc_expression_metrics.Rd man/calc_fdr.Rd man/calc_impres.Rd man/calculate_gene_signatures.Rd man/chao1.Rd man/cjust.Rd man/cluster_group_plot.Rd man/cluster_list_to_df.Rd man/collapse_identical_clusters.Rd man/convert_gmt_file.Rd man/convert_na_to_zeroes.Rd man/convert_piped_col_names_to_single_names.Rd man/correlation_central_element.Rd man/create_gene_lookup.Rd man/dXX_index.Rd man/decode_clms.Rd man/decode_special_char.Rd man/default_ckpt_pairs.Rd man/differential_expression.Rd man/drop_low_columns.Rd man/encode_special_char.Rd man/evenness.Rd man/extract_mixcr_analyze_shotgun_reports.Rd man/find_central_elements_by_cluster.Rd man/find_low_variance_clms.Rd man/find_similar_clms.Rd man/format_gene_set_name.Rd man/format_imported_annotation.Rd man/generate_kmeans_cluster_list.Rd man/get_annotation_indention.Rd man/get_annotation_path.Rd man/get_annotation_width.Rd man/get_biomart_hsa_ucsc_path.Rd man/get_corrected_entropy_rdata_2_4096_path.Rd man/get_corrected_entropy_rdata_4097_65536_path.Rd man/get_corrected_entropy_rdata_ab1025_65K_ent1_8_path.Rd man/get_corrected_entropy_rdata_ab8_1024_ent1_8_path.Rd man/get_default_sample_key.Rd man/get_features_from_gmt_file.Rd man/get_features_from_ranks.Rd man/get_gene_set_entrez_human_bgvlab_path.Rd man/get_gene_set_entrez_human_c2_path.Rd man/get_gene_set_entrez_human_cta_path.Rd man/get_gene_set_entrez_human_kegg_path.Rd man/get_gene_set_hgnc_human_bgvlab_path.Rd man/get_gene_set_hgnc_human_c2cp_path.Rd man/get_gene_set_hgnc_human_cta_path.Rd man/get_gene_set_hgnc_human_kegg_path.Rd man/get_gene_sigs_clustered_by_category.Rd man/get_ipres_gene_sigs.Rd man/get_note_extension.Rd man/get_ranks_from_df.Rd man/get_rho.Rd man/gg_color_hue.Rd man/grapes-ni-grapes.Rd man/group_clusters_by_size.Rd man/has_sufficient_abundance_for_entropy.Rd man/immune_gene_set_groupings.Rd man/import_annotation.Rd man/import_gmt_as_list.Rd man/import_model_data.Rd man/inv_simpson.Rd man/is_not_null.Rd man/isolate_central_cluster_elements.Rd man/ljust.Rd man/log_transform_plus.Rd man/make_intro_text.Rd man/minimal_decimal_places_ordered.Rd man/normalize_rows_by_quartile.Rd man/operatable_columns.Rd man/pc1_vs_pc2_plot.Rd man/pca_central_element.Rd man/pca_variance_plot.Rd man/plot_cumulative_features.Rd man/plot_error_volcano.Rd man/plot_waterfall.Rd man/predict_true_entropy_from_counts.Rd man/predict_true_entropy_from_diversity.Rd man/print_cluster_counts.Rd man/pvalue_nums.Rd man/pvalue_stars.Rd man/regression.Rd man/require_data_in_samples.Rd man/rjust.Rd man/round_data.Rd man/scale_columns.Rd man/screen_counts.Rd man/serial_import.Rd man/shannon_entropy.Rd man/specify_decimal.Rd man/t_test_ci.Rd man/view_boxplot.Rd man/view_clustered_myHeatmap.Rd man/view_volcano_plot.Rd man/wrap_sentence.Rd man/write_central_elements_table.Rd man/write_list_as_gmt.Rd man/write_metadata.Rd man/write_ranked_central_elements_table.Rd man/z_test_ci.Rd