NB                      Draw nonzero negative binomial random numbers
add_error               add sequencing error to simulated reads
add_gc_bias             add GC bias to a count matrix
add_platform_error      Simulate sequencing error using empirical error
                        model
cdnaf                   Model of positional bias that can arise when
                        RNA-seq is performed using protocols relying on
                        cDNA fragmentation.
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
empirical_density       Estimated distribution of fragment lengths
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
loessfit1               Empirical GC bias model, NA06985
loessfit2               Empirical GC bias model, NA12144
loessfit3               Empirical GC bias model, NA12776
loessfit4               Empirical GC bias model, NA18858
loessfit5               Empirical GC bias model, NA20542
loessfit6               Empirical GC bias model, NA20772
loessfit7               Empirical GC bias model, NA20815
model1                  Empirical error model for Illumina Genome
                        Analyzer IIx with Illumina Sequencing Kit v4
                        chemistry, read mate 1 of a pair
model2                  Empirical error model for Illumina Genome
                        Analyzer IIx with Illumina Sequencing Kit v4
                        chemistry, read mate 2 of a pair
model3                  Empirical error model for Illumina Genome
                        Analyzer IIx with Illumina Sequencing Kit v4
                        chemistry, single-end read
model4                  Empirical error model for Illumina Genome
                        Analyzer IIx with TrueSeq SBS Kit v5-GA
                        chemistry, read mate 1 of a pair
model5                  Empirical error model for Illumina Genome
                        Analyzer IIx with TrueSeq SBS Kit v5-GA
                        chemistry, read mate 2 of a pair
model6                  Empirical error model for Illumina Genome
                        Analyzer IIx with TrueSeq SBS Kit v5-GA
                        chemistry, single-end read
model7                  Empirical error model Roche/454 FLX Titanium,
                        single-end read
polyester               Polyester: simulating RNA-seq reads including
                        differential expression
reverse_complement      reverse-complement some fragments
rnaf                    Model of positional bias that can arise when
                        RNA-seq is performed using protocols relying on
                        RNA fragmentation.
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
simulate_experiment_empirical
                        Simulate RNA-seq experiment based on abundances
                        from a data set
write_reads             write sequencing reads to disk
