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immuneSIM
View on CRAN: Click
here
Download and install immuneSIM package within the R console
Install from CRAN:
install.packages("immuneSIM")
Install from Github:
library("remotes")
install_github("cran/immuneSIM")
Install by package version:
library("remotes")
install_version("immuneSIM", "0.8.7")
Attach the package and use:
library("immuneSIM")
Maintained by
Cédric R. Weber
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-09-27
Latest Update: 2019-09-27
Description:
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 ).
How to cite:
Cédric R. Weber (2019). immuneSIM: Tunable Simulation of B- And T-Cell Receptor Repertoires. R package version 0.8.7, https://cran.r-project.org/web/packages/immuneSIM. Accessed 05 Jan. 2025.
Previous versions and publish date:
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Other R packages that immuneSIM depends,
imports, suggests or enhances
Complete documentation for immuneSIM
Functions, R codes and Examples using
the immuneSIM R package
Some associated functions: 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 .
Some associated R codes: add_clone_count.R . calc_vdj_occ.R . codon_replacement.R . codon_replacement_reconstruction.R . combine_into_paired.R . data.R . dropout_VDJ.R . get_AA_freq_distribution.R . hub_seqs_exclusion.R . immuneSIM.R . immuneSim_random.R . immuneSim_standard.R . kmer_occurrence_opt_k_m_gen.R . load_insdel_data.R . make_kmer_dictionary.R . motif_implantation.R . new_insertion_deletion_df.R . noiseify_VDJ_freqs.R . plot_repertoire_A_vs_B.R . plot_report_repertoire.R . plot_report_repertoire_AA_freq.R . plot_report_repertoire_AA_freq_comparative.R . plot_vdj_occ.R . record_shm_events.R . shm_event_reconstruction.R . somatic_hypermutation_sim.R . theme_akbar.R . update_vdj_freqs.R . Full immuneSIM package functions and examples
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