# Simulate RNA-seq reads

## Documentation for package ‘polyester’ version 1.39.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
NB | Draw nonzero negative binomial random numbers
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