Files in ahopki14/immunoSeqR
Tools for analyzing data from Adaptive's ImmunoSeq platform
.gitignore
DESCRIPTION
NAMESPACE
R/biocload.R
R/bleep.R
R/clonality.R
R/delta_stats.R
R/example_ds.R
R/exp_clone.R
R/filter.DataFrame.R
R/filter.tcr.R
R/find_clones.R
R/fisher.R
R/iseqr_aggregate.R
R/iseqr_exp_cl.R
R/iseqr_make_tcr.R
R/iseqr_merge.R
R/iseqr_morisita.R
R/iseqr_order.R
R/iseqr_plot_factor.R
R/iseqr_plot_metrics.R
R/mean_misc.R
R/morisita.R
R/overlap.R
R/richness.R
R/shared.R
R/simpson.R
R/size.R
R/ss2n.R
R/stars.R
R/synonimity.R
R/tcr.R
R/tert.R
R/total.R
README.md
data/ex_tsv.tar.gz
data/example_ds.rda
license.md
man/bleep.Rd
man/clonality.Rd
man/delta_stats.Rd
man/exp_clone.Rd
man/filter.DataFrame.Rd
man/filter.tcr.Rd
man/fisher.Rd
man/iseqr_aggregate.Rd
man/iseqr_exp_cl.Rd
man/iseqr_make_tcr.Rd
man/iseqr_merge.Rd
man/iseqr_morisita.Rd
man/iseqr_order.Rd
man/iseqr_plot_factor.Rd
man/iseqr_plot_metrics.Rd
man/mean_95.Rd
man/mean_only.Rd
man/mean_sd.Rd
man/morisita.Rd
man/overlap.Rd
man/richness.Rd
man/shared.Rd
man/simpson.Rd
man/size.Rd
man/ss2n.Rd
man/stars.Rd
man/synonymity.Rd
man/tcr-class.Rd
man/tert.Rd
man/total.Rd
scripts/core/1_load_data.R
scripts/core/2_expanded_clones.R
scripts/core/3_aggregate.R
scripts/core/4_calculate_metrics.R
scripts/example.R
scripts/old/10_find_public_clones.R
scripts/old/4_plot_confounders.R
scripts/old/5_graph_summary_stats.R
scripts/old/5a_graph_summary_stats_ggplot.R
scripts/old/6_rankplots.R
scripts/old/7_plot_corr.R
scripts/old/8_graph_delta_stats.R
scripts/old/9_expanded_clone_analysis.R
scripts/old/baseline_analysis.R
scripts/old/baseline_expanded_clones.R
scripts/old/baseline_plot_ranks.R
scripts/old/exp_comparison2.R
scripts/old/fisher_expanded.R
scripts/old/mega_analysis.Rmd
scripts/old/misc/add_to_dict.R
scripts/old/misc/convert_ds_to_int.R
scripts/old/misc/exp_comparison.R
scripts/old/misc/fix_bad_columns.R
scripts/old/misc/fix_dict.R
scripts/old/misc/fix_new_primers.R
scripts/old/misc/km_base.R
scripts/old/misc/make_small_ds.R
scripts/old/misc/make_sum.ds.R
scripts/old/olScan.R
scripts/old/old_summary_stats.R
scripts/old/plot_exp_cl_comparison.R
scripts/old/plot_ranks_layout.R
scripts/old/plots.R
scripts/old/process_data.R
scripts/old/rmd/adjuvant.Rmd
scripts/old/rmd/baseline.Rmd
scripts/old/rmd/comparison.Rmd
scripts/old/rmd/ipi.Rmd
scripts/old/rmd/neoadjuvant.Rmd
scripts/old/rmd/pd1.Rmd
scripts/old/rmd/sbrt.Rmd
scripts/old/sbrt/1_load_data.R
scripts/old/sbrt/2_aggregate_data.R
scripts/old/sbrt/3_calculate_summary_stats.R
scripts/old/sbrt/4_plot_confounders.R
scripts/old/sbrt/5_graph_summary_stats.R
scripts/old/sbrt/6_rankplots.R
scripts/old/sbrt/7_plot_corr.R
scripts/old/sbrt/8_graph_delta_stats.R
scripts/old/sbrt/9_expanded_clone_analysis.R
scripts/old/sbrt/plot_stat_by_type.R
scripts/old/sbrt/plot_stat_by_type.R.save
scripts/old/sbrt/plot_stat_trend.R
scripts/old/tumor_overlap.R
shiny/tcrSeqR_shiny.R
