NB                      Draw nonzero negative binomial random numbers
add_error               add sequencing error to simulated reads
count_transcripts       determine how many transcripts are annotated in
                        a FASTA or GTF file
create_read_numbers     Generate a simulated data set based on known
                        model parameters
fpkm_to_counts          Turn FPKMs from a ballgown object into
                        estimated counts for transcripts
generate_fragments      generate a set of fragments from a set of
                        transcripts
getAttributeField       extract a specific field of the "attributes"
                        column of a data frame created from a GTF/GFF
                        file
get_params              Estimate zero-inflated negative binomial
                        parameters from a real dataset
get_reads               get sequencing reads from fragments
gtf_dataframe           data frame (in gtf-inspired format) for
                        chromosome 22, hg19
polyester               Polyester: simulating RNA-seq reads including
                        differential expression
reverse_complement      reverse-complement some fragments
seq_gtf                 Get transcript sequences from GTF file and
                        sequence info
simulate_experiment     simulate RNA-seq experiment using negative
                        binomial model
simulate_experiment_countmat
                        Simulate RNA-seq experiment
write_reads             write sequencing reads to disk
