Man pages for rioualen/EcoliGenes
What the Package Does (One Line, Title Case)
| closest_gene | Get closest genes from genomic positions given a strand |
| convert_coords | Convert genomic coordinates from 96.2 to 96.3 |
| convert_gene | Convert gene names, IDs etc to reference gene symbols or... |
| convert_tf | Get TF names. |
| get_all_genes | Get all genes as reference bnumbers |
| get_all_tfs | Get all TFs |
| get_confirmed_tfs | Get all confirmed TFs from RegulonDB |
| get_downstream_gene | Get next genes bnumbers for a given vector of bnumbers, with... |
| get_gene_bnumber | Convert gene (symbol, ID, or else) to consensus bnumber... |
| get_gene_info | Get reference info from the master table for a given list of... |
| get_gene_length | Get gene nucleotide length |
| get_gene_start | Get gene start |
| get_gene_stop | Get gene stop |
| get_gene_strand | Get gene strand |
| get_gene_symbol | Convert any gene name or id to reference gene symbol... |
| get_gene_synonyms | Get gene synonyms from the master table for a given vector of... |
| get_phantom_genes | Get phantom genes from RegulonDB |
| get_predicted_tfs | Get predicted TFs from the literature (Perez-Rueda 2015,... |
| get_pseudo_genes | Get pseudo genes from RegulonDB |
| get_tf_bnumber | Convert TF protein names into gene bnumbers deprecated |
| get_tf_class | Get class info for a given TF or list of TFs |
| get_tf_effect | Get conformation_type info for a given TF or list of TFs |
| get_tf_family | Get family info for a given TF or list of TFs |
| get_tf_genes | Get TF-coding genes from RegulonDB (does not include putative... |
| get_tf_name | Convert TF protein names into symbols deprecated |
| get_tfs_by_family | Get TFs from a specific family |
| get_tf_symbol | Convert TF protein names into gene symbols deprecated |
| get_tf_symmetry | Get symmetry info for a given TF or list of TFs |
| get_tf_synonyms | Get tf synonyms from the master table for a given vector of... |
| get_upstream_gene | Get previous genes bnumbers for a given vector of genes, with... |
| is_confirmed_tf | Check if TF name is valid |
| is_genic | Check if a position or vector of positions are genic |
| is_phantom_gene | Check if genes are phantom genes |
| is_predicted_tf | Check if TF is predicted (from either Perez-Rueda 2015,... |
| is_pseudo_gene | Check if genes are pseudo genes |
| is_tf | Check if TF name is valid |
| is_tf_gene | Check if genes are TF-coding according to RegulonDB |
| is_valid_bnumber | Check if bnumbers are valid |
| read_coords_file | Read the file that contains genomic coordinates... |
| read_master_gene_file | Read the reference gene file obsolete |
| read_master_tf_file | Read the reference tf file obsolete |
| read_source_file | Read source file |
| what_genes | Get bnumbers from genes entirely comprised in a given... |
| where_genic | Check in which gene falls a given position |
| where_genic_rel | Check where in gene |
