Files in santiago1234/iCodon
iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/data.R
R/evolution.R
R/iCodon.R
R/ml-preprocessing.R
R/optimization.R
R/predict-stability.R
R/runExample.R
R/selection.R
R/shinyscripts.R
R/utilities.R
R/utils-pipe.R
R/visualization.R
README.Rmd
README.md
codecov.yml
data-raw/DATASET.R
data-raw/predict_endogenous_sequences.R
data-raw/sampling_synonimous.R
data-raw/train-predictive-model.R
data-raw/train_test_data.R
data/codones.rda
data/gc_amino_to_codons_l.rda
data/gc_codons_to_amino.rda
data/human_optimality.rda
data/mrna_stability_model.rda
data/optipred.rda
data/preprocessing_recipe.rda
data/sampling_deoptimization.rda
data/sampling_optimization.rda
data/test_seq.rda
data/testing.rda
data/training.rda
hex_logo/hex_logo.R
hex_logo/logo.png
iCodon.Rproj
inst/CITATION
inst/shiny-examples/iCodon/server.R
inst/shiny-examples/iCodon/ui.R
man/add_codon_counts.Rd
man/codon_distance.Rd
man/codones.Rd
man/count_codons.Rd
man/evolution.Rd
man/figures/README-pressure-1.png
man/figures/README-viz-1.png
man/figures/README-viz2-1.png
man/figures/logo.png
man/gc_amino_to_codons_l.Rd
man/gc_codons_to_amino.Rd
man/human_optimality.Rd
man/mrna_stability_model.Rd
man/nucleotide_distance.Rd
man/optimizer.Rd
man/optipred.Rd
man/pipe.Rd
man/plot_optimization.Rd
man/predict_stability.Rd
man/preprocess_secuences.Rd
man/preprocessing_recipe.Rd
man/runExample.Rd
man/run_optimization_shinny.Rd
man/sample_synonimous_codon.Rd
man/sampling_deoptimization.Rd
man/sampling_optimization.Rd
man/selection.Rd
man/split_by_codons.Rd
man/test_seq.Rd
man/testing.Rd
man/training.Rd
man/translate.Rd
man/unscale_decay_to_mouse.Rd
man/validate_sequence.Rd
man/visualize_evolution.Rd
man/viz_result_shiny.Rd
paper/analysis/200317-CodonOptimizationVSoptimality/00-compute-codon-usage.R
paper/analysis/200317-CodonOptimizationVSoptimality/02-plot-compare.R
paper/analysis/200317-CodonOptimizationVSoptimality/README.md
paper/analysis/200317-CodonOptimizationVSoptimality/optimalityVSusage.pdf
paper/analysis/200317-CodonOptimizationVSoptimality/results_data/codon_usage.csv
paper/analysis/200317-CodonOptimizationVSoptimality/results_data/optimality_lasso.csv
tests/testthat.R
tests/testthat/test-evolution.R
tests/testthat/test-optimization.R
tests/testthat/test-predict-stability.R
tests/testthat/test-selection.R
tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/iCodon.Rmd
