| base2kmer | Converts a base representation (base 4 default) to the kmer |
| base5to10 | Converts a base representation (base 4 default) to normal... |
| base5to10_c | Converts a base representation (base 4 default) to normal... |
| build_alphabet | Sets up the alphabet for indexing nucleotides |
| convert10to5 | Converts a normal (base 10) integer to base representation... |
| convert10to5_c | Converts a normal (base 10) integer to base representation... |
| convert10tobase_c | Converts a normal (base 10) integer to base representation... |
| convert10tokmer | Converts a normal (base 10) integer to the equivalent kmer |
| dna_input | Part of a DNA sequence |
| kmer2base | Converts a kmer to a number in base 4 (default) |
| kmer_counter | Represents the kmers present in the input with their integer... |
| kmer_counter_c | Represents the kmers present in the input with their integer... |
| kmer_counter_para_c | Represents the kmers present in the input with their integer... |
| kmer_counter_wrapper | Represents the kmers present in the input with their integer... |
| kmer_counter_wrapper_c | Represents the kmers present in the input with their integer... |
| kmer_dot_prod | Computes the dot product of the parameters with the kmer... |
| kmer_dot_prod_c | Computes the dot product of the parameters with the kmer... |
| kmermods | 'kmermods': Represents Kmers As Integers Along The Genome |
| kmerto10 | Converts a kmer to it's normal (base 10) integer... |
| l1_prox_op | L1 regulatisation proximal operator |
| let2base | Finds the integer that represents the nucleotide |
| let2base_c | Finds the integer that represents the nucleotide |
| loglik_linesearch | Calculates the log likelihood of the data, given some... |
| loglik_logreg | Calculates the log likelihood of the data, given some... |
| loglik_log_reg_grad | Computes the gradient of the log likelihood of a logistic... |
| log_reg_wrapper | Computes the gradient of the log likelihood of a logistic... |
| lower_kmer | Finds the (k-1)mer integer representation ffrom the kmer... |
| mismatch_kmers | Counts the number of mismatches between two kmers, when... |
| params_peaks_noslide | Computes the vector with which to update the parameters in a... |
| params_peaks_noslide_w_error | Computes the vector with which to update the parameters in a... |
| predict_peaks | Computes the predictions for the logistic regression |
| rev_comp | Finds the reverse complementary kmer, in integer form,... |
| rev_comp_c | Finds the reverse complementary kmer, in integer form,... |
| rev_comp_meth | Finds the reverse complementary kmer, in integer form, using... |
| total_error | Computes the total error of the predictions. |
| unwrap_kmers | Takes a longer kmer and converts it into a vector of its... |
| unwrap_kmers_vect | Takes in a single long kmer, for example a 26mer, and returns... |
| update_paras | Creates the update for the parameter vector according to the... |
