Man pages for Benjamin-Vincent-Lab/binfotron
Binfotron Bioinformatics Analysis Tools Suite
| add_comments | Append my_comment to my_dt 'comments' attribute |
| add_filler | Adds a filler to the text. |
| announce_end_of_stack | Announce the ending of a stacked function |
| announce_start_of_stack | Announce the begining of a stacked function |
| announce_total_time | Tells the total time if given a start time. |
| as.bullet | Formats text as a bullet. |
| as.footer | Right justifies and add a filler to the text. |
| as.header1 | Adds horizontal lines above and below the text. |
| as.header2 | Adds filler to the text. |
| balanced_folds | Get indices of a fold of data that balances the distribution... |
| bgv_lab_prep_count_data_for_deseq2 | Preps counts data prior to running gene signature. |
| bgv_lab_prep_count_data_for_gene_signature | Preps counts data prior to running gene signature. |
| binfotron-package | Binfotron Bioinformatics Analysis Tools Suite |
| break_sentence | Inserts newlines into strings after a specified character... |
| calc_expression_metrics | Quantify expression metrics for qc purposes |
| calc_fdr | Performs an FDR calculation on the fdr_on_columns. |
| calc_impres | Calculate an IMPRES score |
| calculate_gene_signatures | Calculate gene signatures on my_dt using a gmt file. |
| chao1 | chao1 |
| cjust | Applies center justification to my_string. |
| cluster_group_plot | Saves to file a plot of the clusters within a cluster group |
| cluster_list_to_df | Reformat a long list of cluster members as a data.frame |
| collapse_identical_clusters | Remove identical clusters |
| convert_gmt_file | Create gene lookup |
| convert_na_to_zeroes | Converts the NA in a data.table or data.frame to zeroes. |
| convert_piped_col_names_to_single_names | Convert piped column names into one of the elements of the... |
| correlation_central_element | Determine the most similar of a list of elements to all other... |
| create_gene_lookup | Create gene lookup |
| decode_clms | Decodes data.frame or data.table using decode_special_char |
| decode_special_char | Decodes unicode hex value |
| default_ckpt_pairs | Get the default gene pairs for the impres calculation |
| differential_expression | Does a differential gene expression analysis. |
| drop_low_columns | Drop my_dt columns are below a certain percentile in value. |
| dXX_index | dXX_index |
| encode_special_char | encodes non alpha numeric or underscore characters into hex. |
| evenness | evenness |
| extract_mixcr_analyze_shotgun_reports | Pull the numbers out of the reports from 'mixcr analyze... |
| find_central_elements_by_cluster | Encapsulation of steps to create clusters and determine most... |
| find_low_variance_clms | Returns column names of those whose most common factor is... |
| find_similar_clms | Finds columns that have a high degree of correlation with... |
| format_gene_set_name | Swaps hyphens for underscores |
| format_imported_annotation | Tabs out an imported annotations to isolate them visually. |
| generate_kmeans_cluster_list | Obtain a list of clusters with their elements from data... |
| get_annotation_indention | Get the indentation string length that should be used for... |
| get_annotation_path | Get the path to the annotation file. |
| get_annotation_width | Get the annotation width that should be used for annotations. |
| get_biomart_hsa_ucsc_path | get_biomart_hsa_ucsc_path |
| get_corrected_entropy_rdata_2_4096_path | get_corrected_entropy_rdata_2_4096_path |
| get_corrected_entropy_rdata_4097_65536_path | get_corrected_entropy_rdata_2_65536_path |
| get_corrected_entropy_rdata_ab1025_65K_ent1_8_path | get_corrected_entropy_rdata_ab1025_65K_ent1 |
| get_corrected_entropy_rdata_ab8_1024_ent1_8_path | get_corrected_entropy_rdata_ab8_1024_ent1_8_path |
| get_default_sample_key | Return the default f the column name for the default sample... |
| get_features_from_gmt_file | get_features_from_gmt_file |
| get_features_from_ranks | Return vector of features names from a data.frame with rank... |
| get_gene_set_entrez_human_bgvlab_path | get_gene_set_entrez_human_bgvlab_path |
| get_gene_set_entrez_human_c2_path | get_gene_set_entrez_human_c2_path |
| get_gene_set_entrez_human_cta_path | get_gene_set_entrez_human_cta_path |
| get_gene_set_entrez_human_kegg_path | get_gene_set_entrez_human_kegg_path |
| get_gene_set_hgnc_human_bgvlab_path | get_gene_set_hgnc_human_bgvlab_path |
| get_gene_set_hgnc_human_c2cp_path | get_gene_set_hgnc_human_c2cp_path |
| get_gene_set_hgnc_human_cta_path | get_gene_set_hgnc_human_cta_path |
| get_gene_set_hgnc_human_kegg_path | get_gene_set_hgnc_human_kegg_path |
| get_gene_sigs_clustered_by_category | Gets the name of the immune gene signatures ordered by cell... |
| get_ipres_gene_sigs | Returns the names of the IPRES gene signatures. |
| get_note_extension | Gets the note extention from the global environment. |
| get_ranks_from_df | function dependencies: |
| get_rho | Run cor.test and passes results |
| gg_color_hue | Get ggplot colors |
| grapes-ni-grapes | Not in |
| group_clusters_by_size | Group a list of clusters by size |
| has_sufficient_abundance_for_entropy | has_sufficient_abundance_for_entropy |
| immune_gene_set_groupings | Lists the immune gene signatures grouped by cell type. |
| import_annotation | Get annotation text at a path location. |
| import_gmt_as_list | Imports a gmt file as a list. |
| import_model_data | Perform common steps needed for importing model data |
| inv_simpson | inv_simpson |
| is_not_null | Is not null |
| isolate_central_cluster_elements | Determine most representative element in each cluster based... |
| ljust | Left justifies my_string. |
| log_transform_plus | Does a log transformation of the data plus a specified value. |
| make_intro_text | Formats intro text for stackable functions |
| minimal_decimal_places_ordered | Reduce decimal places needed |
| normalize_rows_by_quartile | Normalize data values across rows by quartile |
| operatable_columns | Determines what column names can be operated upon. |
| pc1_vs_pc2_plot | Saves to file a plot of pc1 vs pc2 from a pca analysis |
| pca_central_element | Determine the most central of a list of elements based on pca... |
| pca_variance_plot | Saves to file a cumulative variance plot for principle... |
| plot_cumulative_features | Plots a line depicting the number of features ( or any... |
| plot_error_volcano | Creates a scatterplot with optional errorbars and fine... |
| plot_waterfall | Plots a bar graph depicting the hazard ratio ( on log10 scale... |
| predict_true_entropy_from_counts | predict_true_entropy_from_counts |
| predict_true_entropy_from_diversity | predict_true_entropy_from_diversity |
| print_cluster_counts | Display cluster distribution within groups by cluster size |
| pvalue_nums | Return string indicating significance level bin of p.value... |
| pvalue_stars | Turns pvalue into stars |
| regression | performs the specified regression on the data |
| require_data_in_samples | Drop my_dt columns that aren't present in certain... |
| rjust | Right justifies my_string. |
| round_data | Round data.table columns |
| scale_columns | Scales data.table columns. |
| screen_counts | screen_counts |
| serial_import | Import a vector fo file paths into one matrix. |
| shannon_entropy | shannon_entropy |
| soft_scale | Winsorized scaling |
| specify_decimal | String rounded to a specific decimal places |
| t_test_ci | calculates mean & CI for residuals using t-distribution |
| view_boxplot | Create a boxplot of analysis results. |
| view_clustered_myHeatmap | Create a heatmap of analysis results. |
| view_volcano_plot | Create a volcano plot of analysis results. |
| wrap_sentence | Breaks up a string into a character vector with strings of a... |
| write_central_elements_table | Saves to file a dataframe of elements ( i.e. features ) x... |
| write_list_as_gmt | Saves to file list of element combinations and most central... |
| write_metadata | Adds metadata to pdf |
| write_ranked_central_elements_table | Saves to file a dataframe with two columns, Element and Rank |
| z_test_ci | calculates mean & CI for residuals using z-score sd |
