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.

AuthorAlyssa C. Frazee, Andrew E. Jaffe, Rory Kirchner, Jeffrey T. Leek
Date of publicationNone
MaintainerJack Fu <jmfu@jhsph.edu>, Jeff Leek <jtleek@gmail.com>
LicenseArtistic-2.0
Version1.10.0

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

Functions

add_error Man page
add_gc_bias Man page
add_platform_error Man page
cdnaf Man page
count_transcripts Man page
create_read_numbers Man page
empirical_density Man page
fpkm_to_counts Man page
generate_fragments Man page
getAttributeField Man page
get_params Man page
get_reads Man page
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
model1 Man page
model2 Man page
model3 Man page
model4 Man page
model5 Man page
model6 Man page
model7 Man page
NB Man page
polyester Man page
polyester-package Man page
reverse_complement Man page
rnaf Man page
seq_gtf Man page
simulate_experiment Man page
simulate_experiment_countmat Man page
simulate_experiment_empirical Man page
write_reads Man page

Files

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

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