Man pages for jianhong/InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

addChr2ExcludeAdd a globally-applied requirement for filtering out...
addInPASEnsDbAdd a globally defined EnsDb to some InPAS functions.
addInPASGenomeAdd a globally defined genome to all InPAS functions.
addInPASOutputDirectoryAdd a globally defined output directory to some InPAS...
addInPASTxDbAdd a globally defined TxDb for InPAS functions.
addLockNameAdd a filename for locking a SQLite database
adjust_distalCPsAdjust distal CP sites by the cleanUpdTSeq algorithm
adjust_proximalCPsAdjust the proximal CP sites
adjust_proximalCPsByNBCadjust the proximal CP sites by using Naive Bayes classifier...
adjust_proximalCPsByPWMadjust the proximal CP sites by matching PWM
assemble_allCovAssemble coverage files for a given chromosome for all...
assign_featureHelper function to label the last component of a genomic...
calculate_mseCalculate mean squared errors (MSE)
compensationCompensate the coverage with GC-content or mappability
dot-onAttachA function called upon a package is attached to the search...
extract_UTR3Annoextract 3' UTR information from a GenomicFeatures::TxDb...
fft.smoothSmoothing using Fast Discrete Fourier Transform
filter_testOutfilter 3' UTR usage test results
find_minMSEDistrVisualization of MSE profiles, 3' UTR coverage and minimal...
find_valleyBySplineFind major valleys after spline smoothing
gcCompCalculate weights for GC composition
gcContentshelper function to calculate chromosome/scaffold level GC...
getChr2ExcludeGet a globally-applied requirement for filtering scaffolds.
get_chromosomesIdentify chromosomes/scaffolds for CP site discovery
get_depthWeightCalculate the depth weight for each sample or each...
getInPASEnsDbGet the globally defined EnsDb.
getInPASGenomeGet the globally defined genome
getInPASOutputDirectoryGet the path to a output directory for InPAS analysis
getInPASSQLiteDbGet the path to an SQLite database
getInPASTxDbGet the globally defined TxDb.
get_lastCDSUTR3Extract the last unspliced region of each transcript
getLockNameGet the path to a file for locking the SQLite database
get_PAscoreCalculate the CP score
get_PAscore2calculate the CP score
get_regionCovGet coverage for 3' UTR and last CDS regions on a single...
get_seqLenGet sequence lengths for chromosomes/scaffolds
get_ssRleCovGet Rle coverage from a bedgraph file for a sample
get_totalCovCalculate the total coverage
get_usage4plotprepare coverage data and fitting data for plot
get_UTR3CDSGet 3' UTRs and their last CDS regions based on CP sites
get_UTR3eSetprepare 3' UTR coverage data for usage test
get_UTR3regionextract long and short 3UTR region
get_UTR3TotalCovextract coverage of 3' UTR for CP sites prediction
get_zScoreCutoffCalculate local background cutoff value
InPASA package for identifying novel Alternative PolyAdenylation...
mapCompCalculate weights for mappability-base coverage correction
parse_TxDbExtract gene models from a TxDb object
plot_utr3UsageVisualize the dPDUI events using ggplot2
polish_CPspolish the searching results of CP sites
remove_convergentUTR3sremove the converging candidates 3' UTRs LIKE UTR3___UTR3
run_coverageQCQuality control on read coverage over gene bodies and 3UTRs
run_fisherExactTestRun Fisher Exact Test for differential usage of 3' UTRs for a...
run_limmaAnalysisuse limma to analyze the PDUI
run_singleGroupAnalysisdo analysis for single group samples
run_singleSampleAnalysisdo APA analysis for a single sample
search_CPsEstimate the CP sites for UTRs on a given chromosome
search_distalCPssearch distal CP sites
search_proximalCPssearch proximal CPsites
set_globalsSet up global variables for an InPAS analysis
setup_CPsSearchprepare data for predicting cleavage and polyadenylation (CP)...
setup_GSEAprepare files for GSEA analysis
setup_parCPsSearchPrepare data for predicting cleavage and polyadenylation (CP)...
setup_sqlitedbCreate an SQLite database for storing metadata and paths to...
test_dPDUIdo test for dPDUI
trim_seqnamesFilter sequence names from a BSgenome object
UTR3eSet-classUTR3eSet-class and its methods
utr3.mm10Annotation of 3' UTRs for mouse (mm10)
jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.