Man pages for jiang-junyao/IReNA
IReNA
| add_ENSID | add ENSID |
| add_pseudotime | add pseudotime in monocle object to the metadata of the... |
| add_regulation_type | Add regulation type for each gene pair |
| cal_footprint_cuts | Calculate cuts |
| ChscRNA_genes | chicken Gene ID correspondence |
| clustering_Kmeans | clustering DEGs by K-means |
| combine_footprints | Combine all footprints of motifs |
| Converse_GeneIDSymbol | ID change |
| diff_peaks | Identify differential peaks |
| enrich_module | Enrichment analysis of each module |
| extract_expressed_TFs | extract expressed transcription factors |
| filter_ATAC | filter regulatory relationships based on footprints with high... |
| filter_expression_profile | filter expression profile |
| filter_original_regulation | filter original regulation |
| filter_regulation_fimo | Filter regulatory relationships according to binding motifs... |
| filter_regulation_Rcis | Filtering regulatory relationship |
| find_motifs | Find motifs |
| find_motifs_targetgenes | Use fimo to scan the TSS regions of candidate genes to find... |
| Footprints_FOS | Calculate FOS of footprints |
| generate_fimo_regulation | Generate regulation database accoding to the fimo result |
| generate_peak_gtf | Merge peak and generate gft |
| generate_scATAC_Candid | Generate scATAC Candid list |
| get_bed | get bed |
| get_cor | Calculate correlation of each gene pair, and remove genes... |
| get_merged_fasta | merge footprints and return corresponding sequence- |
| Get_p2g_fun | Filter peak-to-gene link |
| get_pseudotime | Calculate pseudotime of cells |
| get_related_genes | Annotate peaks based on regions of peak |
| get_related_peaks | Get candidate genes/TFs-related peaks |
| get_SmoothByBin_PseudotimeExp | Smooth cells into bins based on pseudotime or State |
| get_tss_region | Get tss region sequence of target genes in regulaotry... |
| HsscRNA_genes | homo sapiens Gene ID correspondence |
| identify_region_tfs | Title |
| initiate_cy | initiating the cytoscape |
| irena_step1 | irena_step1 |
| irena_step2 | Title |
| load_counts | load counts |
| merge_sort_count | Merge and sort counts |
| MmscRNA_genes | Mus musculus Gene ID correspondence |
| motifs_select | Select the motif related to the input genes |
| network_analysis | Function to make regulatory network analysis |
| output_grn | Generate grn format regulatory relationships |
| overlap_footprints_peaks | Overlap differential peaks and motif footprints |
| plot_intramodular_network | Function to visualize intramodular regulatory network |
| plot_kmeans_pheatmap | plot kmeans pheatmap |
| plot_tf_network | Function to visualize transcription factors regulatory... |
| sort_TFs_degree | Sort Transcription factor based on degree. |
| Tranfac201803_Ch_MotifTFsF | Tranfac201803 database of Chicken |
| Tranfac201803_Hs_MotifTFsF | Tranfac201803 database of Homo sapiens |
| Tranfac201803_Mm_MotifTFsF | Tranfac201803 database of chicken |
| Tranfac201803_Zf_MotifTFsF | Tranfac201803 database of Mus musculus |
| ZfscRNA_genes | Zebrafish Gene ID correspondence |
