Man pages for snikumbh/archR
Identify Different Architectures of Sequence Elements
| archR | archR: A package for de novo discovery of different sequence... |
| archR_set_config | Set archR run configuration |
| collate_archR_result | Collate raw clusters at the chosen iteration of archR result |
| collate_clusters | Collate sequence IDs from an existing clustering according to... |
| get_clBasVec | Get functions for archR result object |
| get_one_hot_encoded_seqs | Get one-hot encoded sequences |
| get_seqs_clust_list | Retrieve sequence clusters as a list from the sequence labels |
| handle_dir_creation | Handle directory creation |
| make_dinuc_PWMs | Similarly to the PWM-like matrix for mononucleotides, make... |
| make_sinuc_PWMs | Make a PWM-resembling matrix out of a given n-vector |
| plot_arch_for_clusters | Plot cluster architectures as sequence logos. |
| plot_ggheatmap | Plot a given position weight matrix as a heatmap using... |
| plot_ggseqlogo | Visualize a given (PWM) matrix as a sequence logo. |
| plot_ggseqlogo_of_seqs | Plot sequence logo of a collection of sequences |
| prepare_data_from_FASTA | Generate one-hot encoding of sequences given as FASTA file |
| run_archR_UI | Launch archR's graphical user interface |
| seqs_str | Get sequences from the archR result object |
| viz_bas_vec_heatmap_seqlogo | Visualize the NMF basis vectors in a paired heatmap and... |
| viz_seqs_acgt_mat_from_seqs | Visualize raw DNA sequences as an image |
