Introduction | Example data | Cells with multiple heavy chains in single cell data | Identifying clones by sequence identity | Identifying clones by hierarchical clustering | Identifying clones by spectral clustering
Package: scoper 1.6.0.999
Susanna Marquez
scoper: Spectral Clustering-Based Method for Identifying B Cell Clones
Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi:10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi:10.1101/788620>. Gupta NT, et al. (2017) <doi:10.4049/jimmunol.1601850>.
Authors:
scoper_1.6.0.999.tar.gz
scoper_1.6.0.999.zip(r-4.7-x86_64)scoper_1.6.0.999.zip(r-4.7-arm64)scoper_1.6.0.999.zip(r-4.6-x86_64)scoper_1.6.0.999.zip(r-4.6-arm64)scoper_1.6.0.999.zip(r-4.5-x86_64)
scoper_1.6.0.999.tgz(r-4.6-x86_64)scoper_1.6.0.999.tgz(r-4.6-arm64)scoper_1.6.0.999.tgz(r-4.5-arm64)scoper_1.6.0.tgz(r-4.5-x86_64)
scoper_1.6.0.999.tar.gz(r-4.7-arm64)scoper_1.6.0.999.tar.gz(r-4.7-x86_64)scoper_1.6.0.999.tar.gz(r-4.6-arm64)scoper_1.6.0.999.tar.gz(r-4.6-x86_64)
scoper_1.6.0.999.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scoper/json (API)
| # Install 'scoper' in R: |
| install.packages('scoper', repos = c('https://immcantation.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/immcantation/scoper/issues
Last updated from:a3c58ae9e3. Checks:13 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 211 | ||
| linux-devel-x86_64 | WARNING | 230 | ||
| source / vignettes | OK | 286 | ||
| linux-release-arm64 | WARNING | 178 | ||
| linux-release-x86_64 | WARNING | 201 | ||
| macos-release-arm64 | WARNING | 202 | ||
| macos-release-x86_64 | WARNING | 415 | ||
| macos-oldrel-arm64 | WARNING | 190 | ||
| macos-oldrel-x86_64 | WARNING | 410 | ||
| windows-devel-arm64 | WARNING | 304 | ||
| windows-devel-x86_64 | WARNING | 240 | ||
| windows-release-arm64 | WARNING | 276 | ||
| windows-release-x86_64 | WARNING | 200 | ||
| windows-oldrel-x86_64 | WARNING | 194 | ||
| wasm-release | OK | 129 |
Exports:as.data.framehierarchicalClonesidenticalClonesplotplotCloneSummaryprintspectralClonessummary
Dependencies:ade4airralakazamapeBHBiocGenericsBiocParallelBiostringsbitbit64bitopscigarilloclicliprcodetoolscpp11crayondata.tabledigestdiptestdoParalleldplyrfarverfastclusterforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmsigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixnlmepillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4VectorsS7scalessegmentedSeqinfoseqinrshazamsnowspstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
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