Simulate RNA-seq reads


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Documentation for package ‘polyester’ version 1.0.2

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polyester-package Polyester: simulating RNA-seq reads including differential expression
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
NB Draw nonzero negative binomial random numbers
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