Introduction | AbSeq core analyses | Installation | Bioconductor | GitHub | System prerequisites | R package dependencies | Quick start | Datasets | Basic analysis | HTML reports' directory structure | Comparative analysis using multiple datasets | Advanced Examples | Lazy loading | Alternative reporting options | Parallelization | Interpretation of report's figures | Sequence quality analysis | Sequence length | Alignment quality | Insertions, deletions, and mismatches | Abundance and association analysis | V-(D)-J germline abundance | V-J germline associations | Productivity analysis | V-J frameshifts | Stop codons | Indels and mismatches | Diversity analysis | Clonotype-based analysis | Spectratype analysis | Position-specific analysis | Comparative analysis | Over-representation analysis | Overlapping analysis | Multi-sample analysis | Two-sample analysis | Correlation analysis | Clustering analysis | Appendices | Datasets | Session Info | References
Package: abseqR 1.31.0
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:
abseqR_1.31.0.tar.gz
abseqR_1.31.0.zip(r-4.7)abseqR_1.31.0.zip(r-4.6)abseqR_1.31.0.zip(r-4.5)
abseqR_1.31.0.tgz(r-4.6-any)abseqR_1.31.0.tgz(r-4.5-any)
abseqR_1.31.0.tar.gz(r-4.7-any)abseqR_1.31.0.tar.gz(r-4.6-any)
abseqR_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
abseqR/json (API)
| # Install 'abseqR' in R: |
| install.packages('abseqR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/malhamdoosh/abseqr/issues
On BioConductor:abseqR-1.31.0(bioc 3.24)abseqR-1.30.0(bioc 3.23)
sequencingvisualizationreportwritingqualitycontrolmultiplecomparison
Last updated from:b7b630e1a0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 173 | ||
| linux-devel-x86_64 | NOTE | 312 | ||
| source / vignettes | OK | 314 | ||
| linux-release-x86_64 | NOTE | 285 | ||
| macos-release-arm64 | NOTE | 123 | ||
| macos-oldrel-arm64 | NOTE | 128 | ||
| windows-devel | NOTE | 199 | ||
| windows-release | NOTE | 193 | ||
| windows-oldrel | NOTE | 188 | ||
| wasm-release | OK | 177 |
Exports:abseqReportreport
Dependencies:askpassbase64encBHBiocManagerBiocParallelBiocStylebookdownbslibcachemcirclizecliclustercodetoolscolorspacecommonmarkcpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapflexdashboardfontawesomeformatRfsfutile.loggerfutile.optionsgenericsggcorrplotggdendroggplot2GlobalOptionsgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimenlmeopensslotelpermutepillarpkgconfigplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS7sassscalesshapeshinysnowsourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsveganVennDiagramviridisLitewithrxfunxtableyaml
