Files in GreiffLab/immuneSIM
Tunable Simulation of B- And T-Cell Receptor Repertoires
.DS_Store
.readthedocs.yaml
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
R/add_clone_count.R
R/calc_vdj_occ.R
R/codon_replacement.R
R/codon_replacement_reconstruction.R
R/combine_into_paired.R
R/data.R
R/dropout_VDJ.R
R/get_AA_freq_distribution.R
R/hub_seqs_exclusion.R
R/immuneSIM.R
R/immuneSim_random.R
R/immuneSim_standard.R
R/kmer_occurrence_opt_k_m_gen.R
R/load_insdel_data.R
R/make_kmer_dictionary.R
R/motif_implantation.R
R/new_insertion_deletion_df.R
R/noiseify_VDJ_freqs.R
R/plot_repertoire_A_vs_B.R
R/plot_report_repertoire.R
R/plot_report_repertoire_AA_freq.R
R/plot_report_repertoire_AA_freq_comparative.R
R/plot_vdj_occ.R
R/record_shm_events.R
R/shm_event_reconstruction.R
R/somatic_hypermutation_sim.R
R/sysdata.rda
R/theme_akbar.R
R/update_vdj_freqs.R
README.md
additional_data/.DS_Store
additional_data/full_insertions_and_deletion_data.Rdata
docs/.DS_Store
docs/source/.DS_Store
docs/source/.build/.DS_Store
docs/source/.build/doctrees/environment.pickle
docs/source/.build/doctrees/index.doctree
docs/source/.build/doctrees/parameters.doctree
docs/source/.build/doctrees/pattern_injection.doctree
docs/source/.build/doctrees/quickstart.doctree
docs/source/.build/doctrees/simulation.doctree
docs/source/.build/doctrees/somatic_hypermutation.doctree
docs/source/.build/html/.buildinfo
docs/source/.build/html/.nojekyll
docs/source/.build/html/_sources/index.rst.txt
docs/source/.build/html/_sources/parameters.rst.txt
docs/source/.build/html/_sources/pattern_injection.rst.txt
docs/source/.build/html/_sources/quickstart.rst.txt
docs/source/.build/html/_sources/simulation.rst.txt
docs/source/.build/html/_sources/somatic_hypermutation.rst.txt
docs/source/.build/html/_static/ajax-loader.gif
docs/source/.build/html/_static/alabaster.css
docs/source/.build/html/_static/basic.css
docs/source/.build/html/_static/comment-bright.png
docs/source/.build/html/_static/comment-close.png
docs/source/.build/html/_static/comment.png
docs/source/.build/html/_static/custom.css
docs/source/.build/html/_static/doctools.js
docs/source/.build/html/_static/documentation_options.js
docs/source/.build/html/_static/down-pressed.png
docs/source/.build/html/_static/down.png
docs/source/.build/html/_static/file.png
docs/source/.build/html/_static/jquery-3.2.1.js
docs/source/.build/html/_static/jquery.js
docs/source/.build/html/_static/language_data.js
docs/source/.build/html/_static/minus.png
docs/source/.build/html/_static/plus.png
docs/source/.build/html/_static/pygments.css
docs/source/.build/html/_static/searchtools.js
docs/source/.build/html/_static/underscore-1.3.1.js
docs/source/.build/html/_static/underscore.js
docs/source/.build/html/_static/up-pressed.png
docs/source/.build/html/_static/up.png
docs/source/.build/html/_static/websupport.js
docs/source/.build/html/genindex.html
docs/source/.build/html/index.html
docs/source/.build/html/objects.inv
docs/source/.build/html/parameters.html
docs/source/.build/html/pattern_injection.html
docs/source/.build/html/quickstart.html
docs/source/.build/html/search.html
docs/source/.build/html/searchindex.js
docs/source/.build/html/simulation.html
docs/source/.build/html/somatic_hypermutation.html
docs/source/Makefile
docs/source/acknowledgments.rst
docs/source/conf.py
docs/source/images/.DS_Store
docs/source/images/aa_freq.png
docs/source/images/annotation.pdf
docs/source/images/flowchart.png
docs/source/images/immuneSIM_fig1A.png
docs/source/images/k-mer_occ.png
docs/source/images/length_dist.png
docs/source/images/quickstart_aa_freq_mm_igh.png
docs/source/images/quickstart_length_distribution_mm_igh.png
docs/source/images/quickstart_vdj_occurrence_mm_igh.png
docs/source/images/vdj_usage.png
docs/source/index.rst
docs/source/make.bat
docs/source/motif_implantation.rst
docs/source/parameters.rst
docs/source/quickstart.rst
docs/source/report_generation.rst
docs/source/simulation.rst
docs/source/somatic_hypermutation.rst
immuneSIM_0.8.6.tar.gz
immuneSIM_0.8.6.tgz
immuneSIM_0.8.7.tar.gz
immuneSIM_0.8.7.tgz
immuneSIM_0.9.0.tar.gz
immuneSIM_0.9.0.tgz
man/.DS_Store
man/codon_replacement.Rd
man/codon_replacement_reconstruction.Rd
man/combine_into_paired.Rd
man/gen_code.Rd
man/hotspot_df.Rd
man/hub_seqs_exclusion.Rd
man/immuneSIM.Rd
man/insertions_and_deletion_lengths_df.Rd
man/length_dist_simulation.Rd
man/list_example_repertoires.Rd
man/list_germline_genes_allele_01.Rd
man/load_insdel_data.Rd
man/motif_implantation.Rd
man/one_spot_df.Rd
man/plot_repertoire_A_vs_B.Rd
man/plot_report_repertoire.Rd
man/shm_event_reconstruction.Rd
use_cases/immuneML/immuneSIML.R
use_cases/immuneML/immuneSIML_example.yaml
use_cases/immuneML/metadata_full_sim.csv
