Man pages for currocam/toolkit4pySCA
A set of useful functions for performing an Statistical Coupling Analysis from scratch in R and using pySCA
| download_tax_from_ncbi | Create a dataframe with taxonomic information extracted from... |
| eigenspectrum_SCA_positional_coevolution_matrix_plot | Plot the eigenspectrum of the SCA positional coevolution... |
| extract_tidy_df_from_hmmer | Extract a tidy data frame with the hmmer results. |
| extract_tidy_domains_from_xml | extract_tidy_domains_from_xml |
| extract_tidy_hits_from_xml | extract_tidy_hits_from_xml |
| extract_tidy_stats_from_xml | extract_tidy_stats_from_xml |
| global_similarity_matrix_data | It computes the data from the similarity matriz in order to... |
| global_similarity_matrix_heatmap | Plot a heatmap in order to visualize global view of the... |
| import_pySCA_module_using_reticulate | import_pySCA_module_using_reticulate |
| pairwise_sequence_identities_data | It computes the data from the simmilarity matrix in order to... |
| pairwise_sequence_identities_hist | Plot a histogram of all pairwise sequence identities |
| phmmer_HBG2_HUMAN | phmmer_HBG2_HUMAN |
| pipe | Pipe operator |
| position_specific_conservation_data | Position-specific conservation for each position |
| position_specific_conservation_plot | Plot the position-specific conservation values for each... |
| post_request_to_phmer | post_request_to_phmer |
| pySCA_HBG2_HUMAN | pySCA_HBG2_HUMAN |
| quick_AA_search_using_phmmer | quick_AA_search_using_phmmer |
| read_pySCA_pickle | Reads the pickle file produced by pySCA and returns a list of... |
| SCA_correlation_matrix_data | SCA correlation matrix data |
| SCA_positional_coevolution_matrix_components_data | It returns the independent components and the eigenmodes... |
| SCA_positional_coevolution_matrix_eigenvalues_data | Eigenspectrum of the SCA positional coevolution matrix and 10... |
| sequence_correlation_matrix_projections_data | It computes the data from the PCA and IC and creates a tidy... |
| sequence_correlation_matrix_projections_plot | Plot a facet grid projection |
| write_sectors_for_pymol | Write a small script in pymol where you load the PDB file and... |
