Man pages for abelew/stampr
Perform the STAMP analysis
| calculate_nb | Calculate a vector of Nb values from metadata, samples, and... |
| calculate_resiliency | Internal Resiliency Function. |
| convert_cutoffs | I do not really get this function, here is the author's text: |
| dopar | dopar |
| exclude_samples | Plot the calibration curve of the tags observed vs. CFU |
| filter_given_reference | Filter samples using the tags observed in the reference... |
| filter_given_reference_list | This does the real work for filter_given_reference(). |
| filter_tags | Try out some heuristics for filtering the tag data. |
| filter_topn_tags | Keep only the top-n most abundant tags |
| gather_tags_per_replicate | Extract the tags observed in each replicate's reference... |
| get_bottom_vector | Given a vector and set of steps, use rmvhyper to make a new... |
| get_interval_nb | Grab the maximum value from a portion of the nb vector. |
| make_frequency_df | The f(i,s) term in the Nb estimation equation requires... |
| nb_from_tags | Given a tag data structure, calculate the Nb values and put... |
| nb_minimum_search | Search for minima... Another function I don't understand. |
| pipe | Pipe operator |
| plot_calibration | Plot the calibration curve of the tags observed vs. CFU |
| plot_read_density | Make a boxplot of read density |
| predict_cfu | Try out some methods to go from tags/Nb back to CFU. |
| preprocess_stamp | Preprocess raw reads using cutadapt and my little perl... |
| read_csv_tags | Get tags from a csv file |
| read_qiime_otus | Create data structures similar to read_idx using qiime otus. |
| read_tags | Interpret the files produced by my count_idx.pl script. |
| rtisan_nb_from_tags | A partial copying of the getNrNb() function from rtisan. |
| rtisan_nr_nb | This is the top-level function from the authors. I have it... |
| sorted_nb | Calculate Nb values on a set of sorted read/tag vectors. |
| stampr | stampr: Some functions for analyzing sequencing data intended... |
| vector_proportion | Calculate the proprotion of each value in the vector with a... |
