Man pages for TedCCLeung/MotifAnalysis
What the Package Does (One Line, Title Case)
| addLeadingZeros | Add leading zeros to a numerical vector and convert it to... |
| CISBP_families | Dataframe of families of motifs from the CIS-BP database. |
| CISBP_motifset | Motif set from the CIS-BP database. |
| cluster_table_to_list | Convert a cluster table to a list of list object |
| concatenate_FASTA | Concatenate a list of FASTA files |
| concatenate_gff3 | Concatenate a list of GFF3 files |
| denovo_motifset1 | Motif set formed from de novo motif analysis with WEEDER,... |
| df_TFfamily_colors | Dataframe of motif families from the CIS-BP database. |
| enrich_motifs_fisher | Function to clean up .meme motif files. Remove duplicate... |
| enrich_result_summary | Processing of results from fisherEnrichMotif in a directory |
| filter_genes_by_rDEI | Function to filter gene IDs (TAIR IDs) based on daily... |
| genes_to_promoter_Biostring | Function to filter gene IDs (TAIR IDs) based on daily... |
| get_promoters | Function to return Biostring object with input of gene models |
| hclust_motifs | Perform hierarchical clustering of motifs |
| heatmap_from_Fisher | Plot results of Fisher Exact Test as heat maps |
| heatmap_motif_clustering | Plot the result of hierarchical clustering of motifs |
| heatmap_motif_to_CISBP_family | Retrieve the motifs from a motif heatmap |
| heatmap_TF_family | Perform hierarchical clustering of motifs |
| JASPAR_motifset | Motif set from the JASPAR Plants database. |
| make_TAIR10_TxDb | Function to generate a TxDb object from the GenomicFeatures... |
| motif_clean_up | Function to clean up .meme motif files. Remove duplicate... |
| motif_to_CISBP_family | Search which family the most motif belongs to in CISBP |
| motif_to_similar_CISBP | Find similar motifs against the CIS-BP motif database |
| photoperiodic_clusters | Photoperiodic clusters |
| pipe | Pipe operator |
| pivotDFinDir | Merge all the tabular text files in a directory and perform... |
| plot_positional_bias | Plot the result from analyze_positional_bias |
| positional_bias | Analyse positional bias of motifs in a set of DNA sequences |
| positional_bias_subfunc | Analyse positional bias of motifs in a set of DNA sequences |
| rDEI_summary | TAIR10 gene models from Arabidopsis_thaliana.TAIR10.47.gtf |
| read_Fisher_result | Retrieve results from Fisher's Exact Test |
| read_genes | Read a .txt file line by line and return a character vector. |
| run_enrich | Function to perform motif enrichment from motif mapping... |
| run_heatmap | Function to plot motif enrichment results as heat maps |
| run_input | Function to take in motifs and sequences as inputs |
| run_mapping | Function to perform motif mapping |
| run_master | Function to perform motif enrichment pipeline from motifs and... |
| TAIR10_Grange | Grange object from Arabidopsis_thaliana.TAIR10.47.gtf |
| theme_Prism | Theme for imitating Prism |
