Man pages for cparsania/parcutils
Utility Functions To Deal Day To Day Bioinformatics Tasks.
| dot-assign_class_irFinderSdata | Assign class irFinderSdata |
| dot-categorize_diff_ase | Categorize diff ASE in to 'up' and 'down' based on log2FC,... |
| dot-categorize_diff_genes | Categorize diff genes in to 'up' and 'down' based on log2FC,... |
| dot-check_mendate_columns_for_irFinderSdata | Check mandatory columns in a dataframe |
| dot-count_data_convert_NA_to_0 | Convert NA to 0 from into count data for the function... |
| dot-dsr_to_tibble | Convert DESeq result object in to a tibble. |
| dot-filter_df_by_genes | Filter expression matrix (dataframe) by genes (first column). |
| dot-filter_gff | Filter rows from a GFF file. |
| dot-filter_orgdb_by_genetype | Filter selected orgdb columns by gene-type |
| dot-filter_rows_from_count_data | Filter count data using user thresholds for the function... |
| dot-fix_ASE_diff_rslt_columns | Fix column names of the SpliceWiz edgeR output. |
| dot-fix_hm_colors | Given a matrix generate a color scale for a heatmap. |
| dot-generate_a_lineplot | Generate a gene expression line plot. |
| dot-generate_go_emap_plot | Generate a list of GO EMAP plot. |
| dot-get_all_expressed_genes | Get list of all expressed genes from 'x' |
| dot-get_all_named_expression_matrix | Get named list of gene expression matrix for all samples in... |
| dot-get_count_data | Prepare count data for the function 'run_deseq_analysis()' |
| dot-get_gene_groups_for_fc_scatter_plot | Get gene groups for fc scatter plot |
| dot-get_intron_annotations | Get intron annotations |
| dot-get_parcutils_object_example | Obtain an example object of the class parcutils |
| dot-get_parcutils_obj_gene_names | Get the gene names stored in the parcutils object |
| dot-get_sample_information | Prepare sample information for the function... |
| dot-group_replicates_by_sample | Group replicates by samples. |
| dot-is_genes_present_in_obj_parcutils | Check availability of genes in the object of parcutils |
| dot-is_sample_comparsions_present_in_obj_parcutils | Check availability of sample comparisons in the object of... |
| dot-keep_only_enriched_go | Remove items from the list if no enriched terms found. |
| dot-map_granges_metadata | Map metadata (GC, length and seq) to GRanges object. |
| dot-parallel_import_bw_files | Import several bw files using parallel processing. |
| dot-parcutils_assign_intron_identifier | For each intron in the object irFinderSdata assign unique... |
| dot-perform_kemans_cluster | Perform k-means clustering |
| dot-piarwise_upset | Generate upset plots for DEG between a comparison. |
| dot-prepare_parcutils_ir | Prepare object of parcutils_ir from the object of parcutils |
| dot-save_deg_results | Save DEG results in an excel file. |
| dot-save_de_ir_results | Save DE ir results in an excel file. |
| dot-simplify_go | Remove highly similar GO. |
| dot-validate_a_list_of_normalised_matrix | Validate a list of normalised matrix. |
| dot-validate_irfinders_object | Check if the object belongs to class irFinderSdata. |
| dot-validate_parcutils_chip | Validate a class parcutils_chip |
| dot-validate_parcutils_ir_object | Validate parcutils_ir object |
| dot-validate_parcutils_obj | Validate if an object is of class 'parcutils'. |
| EnhancedVolcano2 | Wrapper around 'EnhancedVolcano::EnhancedVolcano()' |
| enrichMsigDB | Perform over representation analysis (ORA) against Molecular... |
| event_region_to_coordinate | Convert event regions to genomic co-ordinates. |
| event_region_to_granges | Convert SpliceWiz's EventRegion column to GRanges object. |
| get_ASE_by_regulation | Get Alternate Splice Events based on their differential... |
| get_ASE_counts_barplot | Generate a barplot showing counts of alternate splice events... |
| get_ASE_data_matrix | Get a data matrix (PSI, logit, z-score) for a given ASE |
| get_ase_data_matrix_heatmap | Generate a heatmap for a given list of ASE. |
| get_ase_volcano_plot | Generate a volcano plot for diff. ASE. |
| get_chip_signal_heatmap | Generate a ChIP signal heatmap for a given sample. #'... |
| get_chip_signal_over_control_heatmap | Generate a ChIP signal heatmap of treatment over control. |
| get_corr_heatbox | Generate a correlation heat plot. |
| get_diff_ASE_count_barplot | Generate a barplot of diff ASE counts. |
| get_diff_gene_count_barplot | Generate a barplot of DEG counts. |
| get_event_annotations | Annotate event names to event length, seq and GC. |
| get_five_prime_flank_motif | Get a seqlogo for flanking region across five prime end of... |
| get_fold_change_matrix | Prepare a fold change matrix |
| get_fold_change_scatter_plot | Compare log2 fold change between two sample comparisons. |
| get_gene_expression_box_plot | Generate a box plot |
| get_gene_expression_heatmap | Generate a heatmap of normalised gene expression values,... |
| get_gene_expression_line_plot | Generate a line plot for gene expression / fold change... |
| get_genes_by_regulation | Get genes based on their differential regulation |
| get_genes_from_event_name | Get gene names from spliceWiz's EventName column. |
| get_go_emap_plot | Perform gene ontology analysis and visualization for DE... |
| get_heatmap_data | Get data from a heatmap in the same order. |
| get_intergenic_signals | Find signal intensity of intergenic regions. |
| get_normalised_expression_matrix | Prepare a matrix of normalised gene expression values. |
| get_pairwise_corr_plot | Get a scatter plot showing correlation between replicates. |
| get_pca_plot | Generate a PCA plot. |
| get_replicates_by_sample | Group replicates by sample - returns list |
| get_rpkm | Calculate RPKM (Reads per kilobase per million). |
| get_star_align_log_summary | Get alignment summary from the output of STAR program. |
| get_star_align_log_summary_plot | Visualise alignment stats in a bar plot |
| get_three_prime_flank_motif | Get a seqlogo for flanking region across three prime end of... |
| get_tpm | Calculate TPM (Tags Per Million). |
| get_upset_intersects | Get intersects of upset plot. |
| get_volcano_plot | Generate a volcano plot. |
| ggsave2 | Wrapper around ggsave. |
| gsea_analysis | Perform GSEA using Molecular Signature Database (MSigDB). |
| gseMsigDB | Perform gene set enrichment analysis against Molecular... |
| import_topn_bed_features | Import top features (ranked by score) from a bed file. |
| make_enriched_heatmap_list | Create a HeatmapList from parcutils_chip. |
| make_parcutils_chip | Construct a parcutils_chip object |
| named_group_split | Split grouped data with names. A wrapper around... |
| normalise_counts | Convert raw read counts in to normalised values. |
| normalised_matrix_to_rpm | Convert normalised matrix into RPM signal |
| parcutils_chip-class | Set class parcutils_chip |
| plot_chip_pairwise_correlation_heatmap | Generate a pairwise correlation for chipseq data. |
| plot_deASE_venn | Plot a venn diagram for diff ASE (using event names or gene... |
| plot_deg_upsets | Generate upset plots for differently expressed genes between... |
| plot_deg_venn | Generate a venn diagram showing overlap between DE genes. |
| plot_regions_relative_to_reference | Generate segment plot to visualize genomic regions related to... |
| print.parcutils | S3 print for object 'parcutils' |
| print.parcutils_ase | S3 print for object 'parcutils_ase' |
| print.parcutils_ir | S3 print for object 'parcutils_ir' |
| run_ase_diff_analysis | Perform ASE diff analysis using edgeR. |
| run_deseq_analysis | Run differential expression (DE) analysis for several... |
| save_go_data | Save GO data in a excel file. |
| save_go_plots | Save GO plot(s) in .pdf files. |
| sort_geom_box | Sort order of box obtained from geom_boxplot |
