Introduction | Bioconductor installation | Devel installation from github | Aligning reads | Gene-transcript matching | DTU pipeline | Preliminary information | Optional (recommended): transcript pre-filtering | Load the data | salmon input | kallisto input | Optional (recommended): infer an informative prior for the precision parameter | Test for DTU | Results in detail | Gene level results | Transcript level results | Inference with 3 or more groups | Inference with 1 group only | Session info | References
Package: BANDITS 1.29.0
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_1.29.0.tar.gz
BANDITS_1.29.0.zip(r-4.7)BANDITS_1.29.0.zip(r-4.6)BANDITS_1.29.0.zip(r-4.5)
BANDITS_1.29.0.tgz(r-4.6-x86_64)BANDITS_1.29.0.tgz(r-4.6-arm64)BANDITS_1.29.0.tgz(r-4.5-x86_64)BANDITS_1.29.0.tgz(r-4.5-arm64)
BANDITS_1.29.0.tar.gz(r-4.7-arm64)BANDITS_1.29.0.tar.gz(r-4.7-x86_64)BANDITS_1.29.0.tar.gz(r-4.6-arm64)BANDITS_1.29.0.tar.gz(r-4.6-x86_64)
BANDITS_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BANDITS/json (API)
| # 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
Datasets:
- 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-1.29.0(bioc 3.24)BANDITS-1.28.0(bioc 3.23)
differentialsplicingalternativesplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationopenblascpp
Last updated from:b8026743da. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 224 | ||
| linux-devel-arm64 | NOTE | 256 | ||
| linux-devel-x86_64 | NOTE | 327 | ||
| source / vignettes | OK | 352 | ||
| linux-release-arm64 | NOTE | 275 | ||
| linux-release-x86_64 | NOTE | 307 | ||
| macos-release-arm64 | NOTE | 188 | ||
| macos-release-x86_64 | NOTE | 432 | ||
| macos-oldrel-arm64 | NOTE | 231 | ||
| macos-oldrel-x86_64 | NOTE | 340 | ||
| windows-devel | NOTE | 267 | ||
| windows-release | NOTE | 262 | ||
| windows-oldrel | NOTE | 421 | ||
| wasm-release | OK | 502 |
Exports:convergencecreate_dataeff_len_computefilter_genesfilter_transcriptsgeneplot_precisionplot_proportionsprior_precisionshowtest_DTUtop_genestop_transcriptstranscript
Dependencies:BHBiocGenericsBiocParallelclicodetoolscpp11data.tabledigestdoParalleldoRNGDRIMSeqedgeRfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobanditeratorslabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSplyrR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloreshape2rlangrngtoolsS4VectorsS7scalesSeqinfosnowstatmodstringistringrvctrsviridisLitewithr
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 |
