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)

# Install 'immuneSIM' in R:

install.packages('immuneSIM', repos = c('https://greifflab.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

4.45 score 38 stars 15 scripts 197 downloads 1 mentions 17 exports 66 dependencies

Last updated 12 months agofrom:eeff4385c9. Checks:OK: 1 FAILURE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 21 2024
R-4.5-linux	FAILURE	Nov 23 2024

Exports:codon_replacement codon_replacement_reconstruction combine_into_paired gen_code hotspot_df hub_seqs_exclusion immuneSIM insertions_and_deletion_lengths_df length_dist_simulation list_example_repertoires list_germline_genes_allele_01 load_insdel_data motif_implantation one_spot_df plot_repertoire_A_vs_B plot_report_repertoire shm_event_reconstruction

Dependencies:askpass BiocGenerics Biostrings cli colorspace cpp11 crayon curl data.table digest fansi farver generics GenomeInfoDb GenomeInfoDbData ggplot2 ggthemes glue gtable httr igraph IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix Metrics mgcv mime munsell nlme openssl pillar pkgconfig plyr poweRlaw pracma purrr R.cache R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp repmis reshape2 rlang S4Vectors scales stringdist stringi stringr sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Help page	Topics
Replaces codons with synonymous codons	codon_replacement
Decodes immuneSIM repertoire codon replacements events.	codon_replacement_reconstruction
Generates a dataframe from separate heavy and light or beta and alpha chain dataframes	combine_into_paired
Translation dictionary amino acid <-> nucleotide codon	gen_code
Hotspot dataframe for SHM	hotspot_df
Deletes top hub sequences from repertoire, changing the network architecture.	hub_seqs_exclusion
Simulates an immune repertoire based on user-defined parameters	immuneSIM
Dataframe containing insertion sequences and deletion lengths	insertions_and_deletion_lengths_df
Vector containing VDJ length distributions	length_dist_simulation
Example repertoires	list_example_repertoires
Collection of germline genes and frequencies	list_germline_genes_allele_01
Loads full insertion/deletion data from GitHub	load_insdel_data
Implant random or predefined motifs into CDR3	motif_implantation
One Spot	one_spot_df
Comparative plots of main repertoire features of two input repertoires (length distribution, amino acid frequency, VDJ usage, kmer occurrence)	plot_repertoire_A_vs_B
Plots main repertoire features (length distribution,amino acid frequencies and VDJ usage)	plot_report_repertoire
Decodes immuneSIM repertoire shm_events column.	shm_event_reconstruction

Package: immuneSIM 0.8.7

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

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