Man pages for alyssafrazee/polyester
Simulate RNA-seq reads

add_erroradd sequencing error to simulated reads
add_gc_biasadd GC bias to a count matrix
add_platform_errorSimulate sequencing error using empirical error model
cdnafModel of positional bias that can arise when RNA-seq is...
count_transcriptsdetermine how many transcripts are annotated in a FASTA or...
create_read_numbersGenerate a simulated data set based on known model parameters
empirical_densityEstimated distribution of fragment lengths
fpkm_to_countsTurn FPKMs from a ballgown object into estimated counts for...
generate_fragmentsgenerate a set of fragments from a set of transcripts
getAttributeFieldextract a specific field of the "attributes" column of a data...
get_paramsEstimate zero-inflated negative binomial parameters from a...
get_readsget sequencing reads from fragments
gtf_dataframedata frame (in gtf-inspired format) for chromosome 22, hg19
loessfit1Empirical GC bias model, NA06985
loessfit2Empirical GC bias model, NA12144
loessfit3Empirical GC bias model, NA12776
loessfit4Empirical GC bias model, NA18858
loessfit5Empirical GC bias model, NA20542
loessfit6Empirical GC bias model, NA20772
loessfit7Empirical GC bias model, NA20815
model1Empirical error model for Illumina Genome Analyzer IIx with...
model2Empirical error model for Illumina Genome Analyzer IIx with...
model3Empirical error model for Illumina Genome Analyzer IIx with...
model4Empirical error model for Illumina Genome Analyzer IIx with...
model5Empirical error model for Illumina Genome Analyzer IIx with...
model6Empirical error model for Illumina Genome Analyzer IIx with...
model7Empirical error model Roche/454 FLX Titanium, single-end read
NBDraw nonzero negative binomial random numbers
polyesterPolyester: simulating RNA-seq reads including differential...
reverse_complementreverse-complement some fragments
rnafModel of positional bias that can arise when RNA-seq is...
seq_gtfGet transcript sequences from GTF file and sequence info
simulate_experimentsimulate RNA-seq experiment using negative binomial model
simulate_experiment_countmatSimulate RNA-seq experiment
simulate_experiment_empiricalSimulate RNA-seq experiment based on abundances from a data...
write_readswrite sequencing reads to disk
alyssafrazee/polyester documentation built on Aug. 5, 2017, 4:11 p.m.