Package: immuneSIM 0.8.7

Cédric R. Weber

immuneSIM: Tunable Simulation of B- And T-Cell Receptor Repertoires

Simulate full B-cell and T-cell receptor repertoires using an in silico recombination process that includes a wide variety of tunable parameters to introduce noise and biases. Additional post-simulation modification functions allow the user to implant motifs or codon biases as well as remodeling sequence similarity architecture. The output repertoires contain records of all relevant repertoire dimensions and can be analyzed using provided repertoire analysis functions. Preprint is available at bioRxiv (Weber et al., 2019 <doi:10.1101/759795>).

Authors:Cédric R. Weber [aut, cre], Victor Greiff [aut]

immuneSIM_0.8.7.tar.gz


immuneSIM_0.8.7.tar.gz(r-4.5-noble)immuneSIM_0.8.7.tar.gz(r-4.4-noble)
immuneSIM_0.8.7.tgz(r-4.4-emscripten)immuneSIM_0.8.7.tgz(r-4.3-emscripten)
immuneSIM.pdf |immuneSIM.html✨
immuneSIM/json (API)

Peer review:

Bug tracker:https://github.com/greifflab/immunesim/issues

On CRAN:

17 exports 37 stars 2.83 score 65 dependencies 1 mentions 15 scripts 254 downloads

Last updated 10 months agofrom:eeff4385c9. Checks:OK: 1 FAILURE: 1. Indexed: yes.

Exports:codon_replacementcodon_replacement_reconstructioncombine_into_pairedgen_codehotspot_dfhub_seqs_exclusionimmuneSIMinsertions_and_deletion_lengths_dflength_dist_simulationlist_example_repertoireslist_germline_genes_allele_01load_insdel_datamotif_implantationone_spot_dfplot_repertoire_A_vs_Bplot_report_repertoireshm_event_reconstruction

Dependencies:askpassBiocGenericsBiostringsclicolorspacecpp11crayoncurldata.tabledigestfansifarverGenomeInfoDbGenomeInfoDbDataggplot2ggthemesgluegtablehttrigraphIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMetricsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpoweRlawpracmapurrrR.cacheR.methodsS3R.ooR.utilsR6RColorBrewerRcpprepmisreshape2rlangS4VectorsscalesstringdiststringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc