Package: HERON 1.11.0

Sean McIlwain

HERON: Hierarchical Epitope pROtein biNding

HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.

Authors:Sean McIlwain [aut, cre], Irene Ong [aut]

HERON_1.11.0.tar.gz
HERON_1.11.0.zip(r-4.7)HERON_1.11.0.zip(r-4.6)HERON_1.11.0.zip(r-4.5)
HERON_1.11.0.tgz(r-4.6-any)HERON_1.11.0.tgz(r-4.5-any)
HERON_1.11.0.tar.gz(r-4.7-any)HERON_1.11.0.tar.gz(r-4.6-any)
HERON_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HERON/json (API)
NEWS

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

Bug tracker:https://github.com/ong-research/heron/issues

Datasets:

On BioConductor:HERON-1.11.0(bioc 3.24)HERON-1.10.0(bioc 3.23)

microarraysoftware

4.00 score 1 stars 8 scripts 275 downloads 41 exports 64 dependencies

Last updated from:bef7869589. Checks:1 NOTE, 9 OK. Indexed: yes.

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linux-devel-x86_64OK441
source / vignettesOK307
linux-release-x86_64OK402
macos-release-arm64OK277
macos-oldrel-arm64OK257
windows-develOK422
windows-releaseOK332
windows-oldrelOK320
wasm-releaseOK140

Exports:.HERONEpitopeDataSet.HERONProbeDataSet.HERONProteinDataSet.HERONSequenceDataSetaddSequenceAnnotationscalcCombPValuescalcEpitopePValuescalcProbePValuesTPairedcalcProbePValuesTUnpairedcalcProbePValuesWUnpairedcalcProteinPValuescatSequencesconvertSequenceDSToProbeDSfindBlocksProbeTfindBlocksTfindEpitopeSegmentsgetEpitopeIDgetEpitopeIDsToProbeIDsgetEpitopeProbeIDsgetEpitopeProteingetEpitopeStartgetEpitopeStopgetKofNgetProteinLabelgetProteinStartgetProteinTilingHERONEpitopeDataSetHERONProbeDataSetHERONProteinDataSetHERONSequenceDataSetlog2TransformmakeEpitopeCallsmakeProbeCallsmakeProteinCallsmin_maxoneHitEpitopesoneHitProbesoneProbeEpitopespvalue_to_zscorequantileNormalizesmoothProbeDS

Dependencies:abindBiobaseBiocGenericsbootclassclassIntclustercodetoolsdata.tableDBIDelayedArraydeldirDEoptimRe1071FMStablegenericsGenomicRangesharmonicmeanpIRangesKernSmoothlatticelimmaMASSmathjaxrMatrixMatrixGenericsMatrixModelsmatrixStatsmetapmnormtmultcompmulttestmutossmvtnormnumDerivplotrixproxyqqconfquantregrbibutilsRcppRdpackrobustbases2S4ArraysS4VectorssandwichSeqinfosfsnspSparseArraySparseMspDataspdepstatmodSummarizedExperimentsurvivalTFisherTH.dataunitswkXVectorzoo

Analyzing High Density Peptide Array Data using HERON

Rendered fromfull_analysis.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-08-22
Started: 2022-10-11

Readme and manuals

Help Manual

Help pageTopics
Add Sequence Annotations for EpitopesaddSequenceAnnotations
Calculate p-values using the "exprs" assaycalcCombPValues
Calculate epitope-level p-valuescalcEpitopePValues
Calculate Probe p-values using a differential paired t-testcalcProbePValuesTPaired
Calculate Probe p-values using a differential unpaired t-testcalcProbePValuesTUnpaired
Calculate Probe p-values using a two-sample wilcoxon testcalcProbePValuesWUnpaired
Calculate protein-level p-valuescalcProteinPValues
Concatenate sequences together based upon their start positions. Assumes the probe sequences have an overlap.catSequences
Convert HERONSequenceDataSet to HERONProbeDataSetconvertSequenceDSToProbeDS
Find Blocks of consecutive probesfindBlocksProbeT
Find consecutive probesfindBlocksT
Find Epitopes from probe stats and calls.findEpitopeSegments
Create EpitopeID from protein, first and last probesgetEpitopeID
Get probe ids from a vector of epitope idsgetEpitopeIDsToProbeIDs
Get the vector of probes from an epitope idgetEpitopeProbeIDs
Obtain Protein Id from Epitope IDgetEpitopeProtein
Obtain first probe's protein start position from Epitope IDgetEpitopeStart
Obtain last probe's protein start position from EpitopeIDgetEpitopeStop
Get K of N statistics from an experiment with padj and callsgetKofN
Get Protein Label from ProbegetProteinLabel
Get the amino-acid starting position of the probe within the protein.getProteinStart
Get Protein TilinggetProteinTiling
SARS CoV-2 Wuhan Peptide Binding Array Dataheffron2021_wuhan
HERONEpitopeDataSet object and constructors.HERONEpitopeDataSet HERONEpitopeDataSet HERONEpitopeDataSet-class
HERONProbeDataSet object and constructors.HERONProbeDataSet HERONProbeDataSet HERONProbeDataSet-class
HERONProteinDataSet object and constructors.HERONProteinDataSet HERONProteinDataSet HERONProteinDataSet-class
HERONSequenceDataSet object and constructors.HERONSequenceDataSet HERONSequenceDataSet HERONSequenceDataSet-class
log2 transform the "exprs" assaylog2Transform
Make Epitope CallsmakeEpitopeCalls
Making Probe-level CallsmakeProbeCalls
Make Protein-level CallsmakeProteinCalls
Cap vector at minimum/maximum valuesmin_max
Find One-hit epitopesoneHitEpitopes
Find one hit probesoneHitProbes
Indicate which epitopes are just one probe.oneProbeEpitopes
Find probe hits with a consecutive probe or another sampleprobeHitSupported
Convert p-value matrix to a z-score matrixpvalue_to_zscore
Normalize the exprs assay using quantile normalizationquantileNormalize
Smooth probes across protein tilingsmoothProbeDS