Package: BANDITS 1.23.0
Simone Tiberi
BANDITS: BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.
Authors:
BANDITS_1.23.0.tar.gz
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BANDITS.pdf |BANDITS.html✨
BANDITS/json (API)
NEWS
| # Install 'BANDITS' in R: |
| install.packages('BANDITS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/simonetiberi/bandits/issues
- gene_tr_id - Gene-transcript matching
- input_data - A 'BANDITS_data' object, generated with 'create_data'
- precision - Estimates for the log-precision parameter
- results - Results of the DTU test, generated with 'test_DTU'
On BioConductor:BANDITS-1.21.0(bioc 3.20)BANDITS-1.20.0(bioc 3.19)
differentialsplicingalternativesplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualization
Last updated 23 days agofrom:46f9bab9ce. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 30 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 30 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 30 2024 |
Exports:convergencecreate_dataeff_len_computefilter_genesfilter_transcriptsgeneplot_precisionplot_proportionsprior_precisionshowtest_DTUtop_genestop_transcriptstranscript
Dependencies:askpassBHBiocGenericsBiocParallelclicodetoolscolorspacecpp11curldata.tabledigestdoParalleldoRNGDRIMSeqedgeRfansifarverforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloreshape2rlangrngtoolsS4VectorsscalessnowstatmodstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BANDITS: Bayesian ANalysis of DIfferenTial Splicing | BANDITS-package BANDITS |
| BANDITS_data class | BANDITS_data BANDITS_data-class show,BANDITS_data-method |
| BANDITS_test class | BANDITS_test BANDITS_test-class convergence convergence,BANDITS_test-method gene gene,BANDITS_test-method plot_proportions plot_proportions,BANDITS_test-method show,BANDITS_test-method top_genes top_genes,BANDITS_test-method top_transcripts top_transcripts,BANDITS_test-method transcript transcript,BANDITS_test-method |
| Create a 'BANDITS_data' object | create_data |
| Compute the median effective length of transcripts. | eff_len_compute |
| Filter lowly abundant genes. | filter_genes |
| Filter lowly abundant transcripts. | filter_transcripts |
| Gene-transcript matching | gene_tr_id |
| A 'BANDITS_data' object, generated with 'create_data' | input_data |
| Plot the log-precision estimates | plot_precision |
| Estimates for the log-precision parameter, generated with 'prior_precision' | precision |
| Infer an informative prior for the precision | prior_precision |
| Results of the DTU test, generated with 'test_DTU' | results |
| Perform differential splicing | test_DTU |