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 |