├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── Class_BANDITS_data.R ├── Class_BANDITS_test.R ├── MCMC_Together.R ├── MCMC_Together_MultiGroup.R ├── MCMC_Unique.R ├── MCMC_Unique_MultiGroup.R ├── MCMC_functions.R ├── RcppExports.R ├── create_data.R ├── data_gene_tr_id.R ├── data_input_data.R ├── data_precision.R ├── data_results.R ├── eff_len_compute.R ├── filter_Genes.R ├── filter_transcripts.R ├── infer_only.R ├── infer_only_Together.R ├── load_kallisto_data.R ├── load_salmon_data.R ├── prior_precision.R ├── roxygen_tags.R ├── run.R ├── run_Multigroup.R └── run_OneGroup.R ├── README.md ├── data ├── gene_tr_id.RData ├── input_data.RData ├── precision.RData └── results.RData ├── inst ├── CITATION ├── extdata │ ├── BANDITS.png │ ├── Homo_sapiens.GRCh38.cdna.all.1.1.10M.fa.gz │ ├── STAR-salmon │ │ ├── sample1 │ │ │ ├── aux_info │ │ │ │ └── eq_classes.txt │ │ │ └── quant.sf │ │ ├── sample2 │ │ │ ├── aux_info │ │ │ │ └── eq_classes.txt │ │ │ └── quant.sf │ │ ├── sample3 │ │ │ ├── aux_info │ │ │ │ └── eq_classes.txt │ │ │ └── quant.sf │ │ └── sample4 │ │ │ ├── aux_info │ │ │ └── eq_classes.txt │ │ │ └── quant.sf │ └── kallisto │ │ ├── sample1 │ │ ├── pseudoalignments.ec │ │ └── pseudoalignments.tsv │ │ ├── sample2 │ │ ├── pseudoalignments.ec │ │ └── pseudoalignments.tsv │ │ ├── sample3 │ │ ├── pseudoalignments.ec │ │ └── pseudoalignments.tsv │ │ └── sample4 │ │ ├── pseudoalignments.ec │ │ └── pseudoalignments.tsv └── script │ └── extdata.Rmd ├── man ├── BANDITS-package.Rd ├── BANDITS_data-class.Rd ├── BANDITS_test-class.Rd ├── create_data.Rd ├── eff_len_compute.Rd ├── filter_genes.Rd ├── filter_transcripts.Rd ├── gene_tr_id.Rd ├── input_data.Rd ├── plot_precision.Rd ├── precision.Rd ├── prior_precision.Rd ├── results.Rd └── test_DTU.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── Rcpp_Together.cpp ├── Rcpp_Together_MultiGroup.cpp ├── Rcpp_Unique.cpp └── Rcpp_Unique_MultiGroup.cpp ├── tests ├── testthat.R └── testthat │ ├── test_create_data.R │ ├── test_eff_len_compute.R │ ├── test_filter_genes.R │ ├── test_filter_transcripts.R │ ├── test_prior_precision.R │ └── test_test_DTU.R └── vignettes ├── BANDITS.Rmd └── References.bib /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimoneTiberi/BANDITS/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimoneTiberi/BANDITS/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SimoneTiberi/BANDITS/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS: 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