polyester: Simulate RNA-seq reads

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.

Author
Alyssa C. Frazee, Andrew E. Jaffe, Rory Kirchner, Jeffrey T. Leek
Date of publication
None
Maintainer
Jack Fu <jmfu@jhsph.edu>, Jeff Leek <jtleek@gmail.com>
License
Artistic-2.0
Version
1.10.0

View on Bioconductor

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

Files in this package

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