polyester-package |
Polyester: simulating RNA-seq reads including differential expression |
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 performed using protocols relying on cDNA fragmentation. |
count_transcripts |
determine how many transcripts are annotated in a FASTA or GTF file |
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 transcripts |
generate_fragments |
generate a set of fragments from a set of transcripts |
getAttributeField |
extract a specific field of the "attributes" column of a data frame created from a GTF/GFF file |
get_params |
Estimate zero-inflated negative binomial parameters from a real dataset |
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 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 |
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 expression |
reverse_complement |
reverse-complement some fragments |
rnaf |
Model of positional bias that can arise when RNA-seq is performed using protocols relying on RNA fragmentation. |
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 set |
write_reads |
write sequencing reads to disk |