polyester: Simulate RNA-seq reads
Version 1.12.0

This package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

AuthorAlyssa C. Frazee, Andrew E. Jaffe, Rory Kirchner, Jeffrey T. Leek
Bioconductor views DifferentialExpression Sequencing
Date of publicationNone
MaintainerJack Fu <jmfu@jhsph.edu>, Jeff Leek <jtleek@gmail.com>
LicenseArtistic-2.0
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("polyester")

Popular man pages

add_gc_bias: add GC bias to a count matrix
empirical_density: Estimated distribution of fragment lengths
fpkm_to_counts: Turn FPKMs from a ballgown object into estimated counts for...
get_params: Estimate zero-inflated negative binomial parameters from a...
loessfit1: Empirical GC bias model, NA06985
simulate_experiment: simulate RNA-seq experiment using negative binomial model
simulate_experiment_countmat: Simulate RNA-seq experiment
See all...

All man pages Function index File listing

Man 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...
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

Functions

NB Man page Source code
add_error Man page Source code
add_gc_bias Man page Source code
add_platform_error Man page Source code
cdnaf Man page
check_error_model Source code
check_extras Source code
check_fold_changes Source code
count_transcripts Man page Source code
create_read_numbers Man page Source code
empirical_density Man page
fpkm_to_counts Man page Source code
generate_fragments Man page Source code
getAttributeField Man page Source code
get_params Man page Source code
get_reads Man page Source code
gtf_dataframe Man page
loessfit1 Man page
loessfit2 Man page
loessfit3 Man page
loessfit4 Man page
loessfit5 Man page
loessfit6 Man page
loessfit7 Man page
makepretty Source code
model1 Man page
model2 Man page
model3 Man page
model4 Man page
model5 Man page
model6 Man page
model7 Man page
polyester Man page
polyester-package Man page
process_custom Source code
reverse_complement Man page Source code
rnaf Man page
seq_gtf Man page Source code
sgseq Source code
simulate_experiment Man page Source code
simulate_experiment_countmat Man page Source code
simulate_experiment_empirical Man page Source code
write_info Source code
write_reads Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/NB.R
R/add_error.R
R/add_gc_bias.R
R/add_platform_error.R
R/cdnaf.R
R/check_extras.R
R/count_transcripts.R
R/create_read_numbers.R
R/empirical_density.R
R/fpkm_to_counts.R
R/generate_fragments.R
R/getAttributeField.R
R/get_params.R
R/get_reads.R
R/gtf_dataframe.R
R/loessfit1.R
R/loessfit2.R
R/loessfit3.R
R/loessfit4.R
R/loessfit5.R
R/loessfit6.R
R/loessfit7.R
R/model1.R
R/model2.R
R/model3.R
R/model4.R
R/model5.R
R/model6.R
R/model7.R
R/polyester-package.R
R/reverse_complement.R
R/rnaf.R
R/seq_gtf.R
R/sgseq.R
R/simulate_experiment.R
R/simulate_experiment_countmat.R
R/simulate_experiment_empirical.R
R/write_reads.R
build
build/vignette.rds
data
data/cdnaf.rda
data/datalist
data/empirical_density.rda
data/gtf_dataframe.rda
data/ill100v4_mate1.rda
data/ill100v4_mate2.rda
data/ill100v4_single.rda
data/ill100v5_mate1.rda
data/ill100v5_mate2.rda
data/ill100v5_single.rda
data/loessfit1.rda
data/loessfit2.rda
data/loessfit3.rda
data/loessfit4.rda
data/loessfit5.rda
data/loessfit6.rda
data/loessfit7.rda
data/rnaf.rda
inst
inst/doc
inst/doc/polyester.R
inst/doc/polyester.Rmd
inst/doc/polyester.html
inst/extdata
inst/extdata/bg.gtf.gz
inst/extdata/chr22.fa
inst/extdata/toy.fa
man
man/NB.Rd
man/add_error.Rd
man/add_gc_bias.Rd
man/add_platform_error.Rd
man/cdnaf.Rd
man/count_transcripts.Rd
man/create_read_numbers.Rd
man/empirical_density.Rd
man/fpkm_to_counts.Rd
man/generate_fragments.Rd
man/getAttributeField.Rd
man/get_params.Rd
man/get_reads.Rd
man/gtf_dataframe.Rd
man/loessfit1.Rd
man/loessfit2.Rd
man/loessfit3.Rd
man/loessfit4.Rd
man/loessfit5.Rd
man/loessfit6.Rd
man/loessfit7.Rd
man/model1.Rd
man/model2.Rd
man/model3.Rd
man/model4.Rd
man/model5.Rd
man/model6.Rd
man/model7.Rd
man/polyester.Rd
man/reverse_complement.Rd
man/rnaf.Rd
man/seq_gtf.Rd
man/simulate_experiment.Rd
man/simulate_experiment_countmat.Rd
man/simulate_experiment_empirical.Rd
man/write_reads.Rd
vignettes
vignettes/polyester.Rmd
polyester documentation built on May 20, 2017, 9:49 p.m.

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