| 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... |
| count_transcripts | determine how many transcripts are annotated in a FASTA or... |
| 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... |
| generate_fragments | generate a set of fragments from a set of transcripts |
| getAttributeField | extract a specific field of the "attributes" column of a data... |
| get_params | Estimate zero-inflated negative binomial parameters from a... |
| 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... |
| model2 | Empirical error model for Illumina Genome Analyzer IIx with... |
| model3 | Empirical error model for Illumina Genome Analyzer IIx with... |
| model4 | Empirical error model for Illumina Genome Analyzer IIx with... |
| model5 | Empirical error model for Illumina Genome Analyzer IIx with... |
| model6 | Empirical error model for Illumina Genome Analyzer IIx with... |
| model7 | Empirical error model Roche/454 FLX Titanium, single-end read |
| NB | Draw nonzero negative binomial random numbers |
| polyester | Polyester: simulating RNA-seq reads including differential... |
| reverse_complement | reverse-complement some fragments |
| rnaf | Model of positional bias that can arise when RNA-seq is... |
| 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... |
| write_reads | write sequencing reads to disk |
