# A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

## Documentation for package ‘InPAS’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | UTR3eSet-class and its methods
$<--method | UTR3eSet-class and its methods
assemble_allCov | Assemble coverage files for all samples
coerce-method | UTR3eSet-class and its methods
extract_UTR3Anno | extract 3' UTR information from a GenomicFeatures::TxDb object
filter_testOut | filter 3' UTR usage test results
get_regionCov | Get coverage for 3' UTR and last CDS regions on a single chromosome
get_ssRleCov | Get Rle coverage from a bedgraph file for a sample
get_usage4plot | prepare coverage data and fitting data for plot
get_UTR3eSet | prepare 3' UTR coverage data for usage test
InPAS | A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq data
parse_TxDb | Extract gene models from a TxDb object
plot_utr3Usage | Visualize the dPDUI events using ggplot2
run_coverageQC | Quality control on read coverage over gene bodies and 3UTRs
search_CPs | Estimate the CP sites for UTRs on a given chromosome
setup_CPsSearch | prepare data for predicting cleavage and polyadenylation (CP) sites
setup_GSEA | prepare files for GSEA analysis
setup_sqlitedb | Create an SQLite database for storing metadata and paths to coverage files
show-method | UTR3eSet-class and its methods
test_dPDUI | do test for dPDUI
utr3.mm10 | Annotation of 3' UTRs for mouse (mm10)
UTR3eSet-class | UTR3eSet-class and its methods