Package: polyester 1.41.0

Jack Fu

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.

Authors:Alyssa C. Frazee, Andrew E. Jaffe, Rory Kirchner, Jeffrey T. Leek

polyester_1.41.0.tar.gz
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polyester.pdf |polyester.html✨
polyester/json (API)
NEWS

# Install 'polyester' in R:
install.packages('polyester', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • cdnaf - Model of positional bias that can arise when RNA-seq is performed using protocols relying on cDNA fragmentation.
  • empirical_density - Estimated distribution of fragment lengths
  • 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 Illumina Sequencing Kit v4 chemistry, read mate 1 of a pair
  • model2 - Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, read mate 2 of a pair
  • model3 - Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, single-end read
  • model4 - Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 1 of a pair
  • model5 - Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 2 of a pair
  • model6 - Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, single-end read
  • rnaf - Model of positional bias that can arise when RNA-seq is performed using protocols relying on RNA fragmentation.

On BioConductor:polyester-1.41.0(bioc 3.20)polyester-1.39.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

17 exports 1.64 score 21 dependencies 3 mentions

Last updated 2 months agofrom:04d9723f88

Exports:add_erroradd_gc_biasadd_platform_errorcount_transcriptscreate_read_numbersfpkm_to_countsgenerate_fragmentsget_paramsget_readsgetAttributeFieldNBreverse_complementseq_gtfsimulate_experimentsimulate_experiment_countmatsimulate_experiment_empiricalwrite_reads

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitelimmalogsplinemimeopensslR6S4VectorsstatmodsysUCSC.utilsXVectorzlibbioc

The Polyester package for simulating RNA-seq reads

Rendered frompolyester.Rmdusingknitr::knitron Jul 02 2024.

Last update: 2021-09-01
Started: 2014-10-03

Readme and manuals

Help Manual

Help pageTopics
add sequencing error to simulated readsadd_error
add GC bias to a count matrixadd_gc_bias
Simulate sequencing error using empirical error modeladd_platform_error
Model of positional bias that can arise when RNA-seq is performed using protocols relying on cDNA fragmentation.cdnaf
determine how many transcripts are annotated in a FASTA or GTF filecount_transcripts
Generate a simulated data set based on known model parameterscreate_read_numbers
Estimated distribution of fragment lengthsempirical_density
Turn FPKMs from a ballgown object into estimated counts for transcriptsfpkm_to_counts
generate a set of fragments from a set of transcriptsgenerate_fragments
Estimate zero-inflated negative binomial parameters from a real datasetget_params
get sequencing reads from fragmentsget_reads
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF filegetAttributeField
data frame (in gtf-inspired format) for chromosome 22, hg19gtf_dataframe
Empirical GC bias model, NA06985loessfit1
Empirical GC bias model, NA12144loessfit2
Empirical GC bias model, NA12776loessfit3
Empirical GC bias model, NA18858loessfit4
Empirical GC bias model, NA20542loessfit5
Empirical GC bias model, NA20772loessfit6
Empirical GC bias model, NA20815loessfit7
Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, read mate 1 of a pairmodel1
Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, read mate 2 of a pairmodel2
Empirical error model for Illumina Genome Analyzer IIx with Illumina Sequencing Kit v4 chemistry, single-end readmodel3
Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 1 of a pairmodel4
Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, read mate 2 of a pairmodel5
Empirical error model for Illumina Genome Analyzer IIx with TrueSeq SBS Kit v5-GA chemistry, single-end readmodel6
Empirical error model Roche/454 FLX Titanium, single-end readmodel7
Draw nonzero negative binomial random numbersNB
Polyester: simulating RNA-seq reads including differential expressionpolyester
reverse-complement some fragmentsreverse_complement
Model of positional bias that can arise when RNA-seq is performed using protocols relying on RNA fragmentation.rnaf
Get transcript sequences from GTF file and sequence infoseq_gtf
simulate RNA-seq experiment using negative binomial modelsimulate_experiment
Simulate RNA-seq experimentsimulate_experiment_countmat
Simulate RNA-seq experiment based on abundances from a data setsimulate_experiment_empirical
write sequencing reads to diskwrite_reads