Package: HERON 1.3.0

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_1.3.0.tar.gz
HERON_1.3.0.zip(r-4.5)HERON_1.3.0.zip(r-4.4)HERON_1.3.0.zip(r-4.3)
HERON_1.3.0.tgz(r-4.4-any)HERON_1.3.0.tgz(r-4.3-any)
HERON_1.3.0.tar.gz(r-4.5-noble)HERON_1.3.0.tar.gz(r-4.4-noble)
HERON_1.3.0.tgz(r-4.4-emscripten)HERON_1.3.0.tgz(r-4.3-emscripten)
HERON.pdf |HERON.html✨
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:

heffron2021_wuhan - SARS CoV-2 Wuhan Peptide Binding Array Data

On BioConductor:HERON-1.3.0(bioc 3.20)HERON-1.2.0(bioc 3.19)

bioconductor-package

40 exports 0.49 score 76 dependencies

Last updated 2 months agofrom:171bac7554

Exports:.HERONEpitopeDataSet .HERONProbeDataSet .HERONProteinDataSet .HERONSequenceDataSet addSequenceAnnotations calcCombPValues calcEpitopePValues calcProbePValuesTPaired calcProbePValuesTUnpaired calcProteinPValues catSequences convertSequenceDSToProbeDS findBlocksProbeT findBlocksT findEpitopeSegments getEpitopeID getEpitopeIDsToProbeIDs getEpitopeProbeIDs getEpitopeProtein getEpitopeStart getEpitopeStop getKofN getProteinLabel getProteinStart getProteinTiling HERONEpitopeDataSet HERONProbeDataSet HERONProteinDataSet HERONSequenceDataSet log2Transform makeEpitopeCalls makeProbeCalls makeProteinCalls min_max oneHitEpitopes oneHitProbes oneProbeEpitopes pvalue_to_zscore quantileNormalize smoothProbeDS

Dependencies:abind askpass Biobase BiocGenerics boot class classInt cluster codetools crayon curl data.table DBI DelayedArray deldir DEoptimR e1071 FMStable GenomeInfoDb GenomeInfoDbData GenomicRanges harmonicmeanp httr IRanges jsonlite KernSmooth lattice limma magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats metap mime mnormt multcomp multtest mutoss mvtnorm numDeriv openssl plotrix proxy qqconf quantreg R6 rbibutils Rcpp Rdpack robustbase s2 S4Arrays S4Vectors sandwich sf sn sp SparseArray SparseM spData spdep statmod SummarizedExperiment survival sys TFisher TH.data UCSC.utils units wk XVector zlibbioc zoo

Analyzing High Density Peptide Array Data using HERON

Rendered fromfull_analysis.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-31
Started: 2022-10-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add Sequence Annotations for Epitopes	addSequenceAnnotations
Calculate p-values using the "exprs" assay	calcCombPValues
Calculate epitope-level p-values	calcEpitopePValues
Calculate Probe p-values using a differential paired t-test	calcProbePValuesTPaired
Calculate Probe p-values using a differential unpaired t-test	calcProbePValuesTUnpaired
Calculate protein-level p-values	calcProteinPValues
Concatenate sequences together based upon their start positions. Assumes the probe sequences have an overlap.	catSequences
Convert HERONSequenceDataSet to HERONProbeDataSet	convertSequenceDSToProbeDS
Find Blocks of consecutive probes	findBlocksProbeT
Find consecutive probes	findBlocksT
Find Epitopes from probe stats and calls.	findEpitopeSegments
Create EpitopeID from protein, first and last probes	getEpitopeID
Get probe ids from a vector of epitope ids	getEpitopeIDsToProbeIDs
Get the vector of probes from an epitope id	getEpitopeProbeIDs
Obtain Protein Id from Epitope ID	getEpitopeProtein
Obtain first probe's protein start position from Epitope ID	getEpitopeStart
Obtain last probe's protein start position from EpitopeID	getEpitopeStop
Get K of N statistics from an experiment with padj and calls	getKofN
Get Protein Label from Probe	getProteinLabel
Get the amino-acid starting position of the probe within the protein.	getProteinStart
Get Protein Tiling	getProteinTiling
SARS CoV-2 Wuhan Peptide Binding Array Data	heffron2021_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" assay	log2Transform
Make Epitope Calls	makeEpitopeCalls
Making Probe-level Calls	makeProbeCalls
Make Protein-level Calls	makeProteinCalls
Cap vector at minimum/maximum values	min_max
Find One-hit epitopes	oneHitEpitopes
Find one hit probes	oneHitProbes
Indicate which epitopes are just one probe.	oneProbeEpitopes
Find probe hits with a consecutive probe or another sample	probeHitSupported
Convert p-value matrix to a z-score matrix	pvalue_to_zscore
Normalize the exprs assay using quantile normalization	quantileNormalize
Smooth probes across protein tiling	smoothProbeDS