Package: abseqR 1.23.0

JiaHong Fong

abseqR: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

Authors:JiaHong Fong [cre, aut], Monther Alhamdoosh [aut]

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abseqR.pdf |abseqR.html✨
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NEWS

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

Peer review:

Bug tracker:https://github.com/malhamdoosh/abseqr/issues

On BioConductor:abseqR-1.23.0(bioc 3.20)abseqR-1.22.0(bioc 3.19)

bioconductor-package

2 exports 0.61 score 101 dependencies

Last updated 2 months agofrom:c25bd7462a

Exports:abseqReportreport

Dependencies:askpassbase64encBHBiocManagerBiocParallelBiocStylebookdownbslibcachemcirclizecliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapflexdashboardfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggcorrplotggdendroggplot2GlobalOptionsgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownsassscalesshapeshinysnowsourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsveganVennDiagramviridisLitewithrxfunxtableyaml

abseqR: reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Jia Hong Fong, Monther Alhamdoosh

Rendered fromabseqR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-10-24
Started: 2018-07-27

Readme and manuals

Help Manual

Help pageTopics
Conducts abundance analysis.abundanceAnalysis
Abundance distribution.abundancePlot
Plots all 5 alignment quality heatmaps.alignQualityHeatMaps
Collect primer names from FASTA.allPrimerNames
Plots amino acid composition logo.aminoAcidBar
Composition logo plot.aminoAcidPlot
Plots the validity of upstream sequences.analyzeUpstreamValidity
Annotation analysis.annotAnalysis
Accessor for 'alignlen' slot.asRepertoireAlignLen
Accessor for 'bitscore' slot.asRepertoireBitscore
Accessor for 'chain' slot.asRepertoireChain
Accessor for the 'outdir' slot.asRepertoireDir
Accessor for AbSeqCRep's list of AbSeqRep objects.asRepertoireList
Accessor for the 'name' slot.asRepertoireName
Accessor for the 'primer3end' slot.asRepertoirePrimer3
Accessor for the 'primer5end' slot.asRepertoirePrimer5
Accessor for 'qstart' slot.asRepertoireQueryStart
Accessor for 'sstart' slot.asRepertoireSubjectStart
Accessor for the 'upstream' slot.asRepertoireUpstream
Creates a box plot.boxPlot
Calculates the "standard" diversity indices.calculateDInd
Calculates Lower Bound Estimates for unseen species and Common Diversity Indices from clonotype tables.calculateDiversityEstimates
Convert file names to human friendly text.canonicalizeTitle
Helper function to capitalize the first letter of 'str'.capitalize
Checks if abseqPy has a metadata line that suggests the orientation.checkVert
Marginal histogram of clonotypes (blue for shared, grey for total). The y axis is scaled by sqrt (but it doesn't really matter anyway, since we're stripping away the y-ticks).cloneDistHist
Marginal density graph of clonotypes (blue for shared, grey for total, purple for exclusive clones).cloneDistMarginal
Comprehensive clonotype analyses.clonotypeAnalysis
Collate all HTML reports into a single directory and cretate an entry 'index.html' file that redirects to all collated HTML files.collateReports
Collect the intersection of all primer names within a collection of primer files.commonPrimerNames
Conducts pearson and spearman correlation analysis on dataframe.correlationTest
Computes the distance between pariwise samples.distanceMeasure
Title Diversity analysis.diversityAnalysis
Creates and returns an empty plot.emptyPlot
Given a directory = <abseqPy_outputdir>/RESULT_DIR/, returns the directories (repositories) in 'directory'. That is, will not return any sample_vs_sample directories. This is done by asserting that a 'repository' must have an (analysis.params) file, and a summary.txt file..findRepertoires
Generates all FR/CDR spectratypes.generateAllSpectratypes
Generates report for all samples in 'compare'.generateDelayedReport
Generates HTML report from 'AbSeqRep' and 'AbSeqCRep' ojects.generateReport
Helper function to return line types by importance based on provided CD/Fs regions.getLineTypes
Get total number of samples (n).getTotal
Plots a plotly heatmap from provided matrix.hmFromMatrix
Returns all samples found under 'sampleDirectory'.inferAnalyzed
Given a dataframe with the columns "from", "to", and value.var, return a symmetric matrix (with diagonal values = diag). I.e. a call to isSymmetric(return_value_of_this_function) will always be TRUE..loadMatrixFromDF
Loads AbSeqCRep or AbSeqRep objects from a list of sampleNames.loadSamplesFromString
Conduct all vs all pairwise comparison analyses.pairwiseComparison
V-J association plot.plotCirclize
Bar plotter.plotDist
Plots rarefaction, recapture, and de-dup plots for specified 'region'.plotDiversityCurves
Duplication level plot.plotDuplication
Plots the error distribution for each region: CDRs, FRs, IGV, IGD, and IGJ.plotErrorDist
Plots the error distribution for IGV germlines.plotIGVErrors
Plot IGV family distribution for a given 'upstreamLengthRange'.plotIGVUpstreamLenDist
Plots the detailed length distribution for IGV families.plotIGVUpstreamLenDistDetailed
Plots, for a given 'category' and 'pend', the 'primer' IGV indelled distribution in a bar plot.plotPrimerIGVStatus
Plots the distribution of primer integrity for a given 'category' and 5' or 3' 'pend'.plotPrimerIntegrity
Rarefaction plot.plotRarefaction
Plots capture-recapture.plotRecapture
Monolith AbSeq Plot function - the "driver" program.plotSamples
Spectratype plotter.plotSpectratype
Plot upstream distribution.plotUpstreamLength
Plot upstream sequence length distribution for upstream sequences (5'UTR or secretion signal) for a given 'upstreamLengthRange'.plotUpstreamLengthDist
Conducts primer specificity analysis.primerAnalysis
Plots a distribution plot for different productivity analysis files.prodDistPlot
Conducts productivty analysis.productivityAnalysis
Summary of productivity.productivityPlot
Return value specifed by key from AbSeq's summary file.readSummary
Title Shows varying regions for a given clonotype defined by its CDR3.regionAnalysis
Reports abundance-based (Lower bound) diversity estimates using the Vegan package.reportLBE
Saves ggplot object as a Rdata file..saveAs
Title Creates a scatter plot.scatterPlot
Creates a complex scatter plot.scatterPlotComplex
Secretion signal analysis.secretionSignalAnalysis
Substitutes the first occurance of `key` with `value` in `filename`.substituteStringInFile
Summary of dataframe.summarySE
Title Clonotype table.topNDist
5' UTR analysis.UTR5Analysis
Title Creates Venndiagram for clonotype intersection.vennIntersection
Combines 2 AbSeqCRep objects together for comparison+,AbSeqCRep,AbSeqCRep-method
Combines a AbSeqCRep object with a AbSeqRep object together for comparison+,AbSeqCRep,AbSeqRep-method
Combines a AbSeqRep object with a AbSeqCRep object together for comparison+,AbSeqRep,AbSeqCRep-method
Combines 2 AbSeqRep objects together for comparison+,AbSeqRep,AbSeqRep-method
S4 class - AbSeqCompositeRepertoire analysis objectAbSeqCRep AbSeqCRep-class
S4 class - AbSeqRepertoire analysis objectAbSeqRep AbSeqRep-class
Visualize all analysis conducted by abseqPyabseqReport
Plots AbSeqRep or AbSeqCRep object to the specfied directoryreport report,AbSeqCRep-method report,AbSeqRep-method