Package: BiBitR 0.4.2
BiBitR: R Wrapper for Java Implementation of BiBit
A simple R wrapper for the Java BiBit algorithm from "A biclustering algorithm for extracting bit-patterns from binary datasets" from Domingo et al. (2011) <doi:10.1093/bioinformatics/btr464>. An simple adaption for the BiBit algorithm which allows noise in the biclusters is also introduced as well as a function to guide the algorithm towards given (sub)patterns. Further, a workflow to derive noisy biclusters from discoverd larger column patterns is included as well.
Authors:
BiBitR_0.4.2.tar.gz
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BiBitR.pdf |BiBitR.html✨
BiBitR/json (API)
| # Install 'BiBitR' in R: |
| install.packages('BiBitR', repos = c('https://ewouddt.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ewouddt/bibitr/issues
Last updated 7 years agofrom:e5fde22dcb. Checks:1 OK, 8 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 05 2025 |
| R-4.5-win | WARNING | Mar 05 2025 |
| R-4.5-mac | WARNING | Mar 05 2025 |
| R-4.5-linux | WARNING | Mar 05 2025 |
| R-4.4-win | WARNING | Mar 05 2025 |
| R-4.4-mac | WARNING | Mar 05 2025 |
| R-4.4-linux | WARNING | Mar 05 2025 |
| R-4.3-win | WARNING | Mar 05 2025 |
| R-4.3-mac | WARNING | Mar 05 2025 |
Exports:bibitbibit_columnextensionbibit2bibit3bibit3_patternBCBiBitWorkflowClusterRowCoverageColInfoColNoiseBCCompareResultJIExactFisherBCmake_arff_row_colMaxBCNoiseInfoBCNoiseScreeRowTest_FishersummaryUpdateBiclust_RowNoise
Dependencies:additivityTestsbiclustclasscliclustercolorspacecpp11curldendextenddplyrfansifarverflexclustforeigngenericsggplot2gluegridExtragtableisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmodeltoolsmunsellnlmepillarpkgconfigpurrrR6randomcoloRRColorBrewerRcpprlangRtsnescalesstringistringrtibbletidyrtidyselectutf8V8vctrsviridisviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The BiBit Algorithm | bibit |
| Column Extension Procedure | bibit_columnextension |
| The BiBit Algorithm with Noise Allowance | bibit2 |
| The BiBit Algorithm with Noise Allowance guided by Provided Patterns. | bibit3 |
| Extract BC from 'bibit3' result and add pattern | bibit3_patternBC |
| A biclustering algorithm for extracting bit-patterns from binary datasets | BiBitR-package BiBitR |
| BiBit Workflow | BiBitWorkflow |
| Row Coverage Plots | ClusterRowCoverage |
| Column Info of Biclusters | ColInfo |
| Barplots of Column Noise for Biclusters | ColNoiseBC |
| Compare Biclustering Results using Jaccard Index | CompareResultJI |
| Apply Fisher Exact Test on Biclusters of a Biclust object | ExactFisherBC |
| Transform R matrix object to BiBit input files. | make_arff_row_col |
| Finding Maximum Size Biclusters | MaxBC |
| Noise Info for Biclusters | NoiseInfoBC |
| Noise Scree Plots | NoiseScree |
| Apply Fisher Exact Test on Bicluster Rows | RowTest_Fisher |
| Summary Method for Biclust Class | summary,Biclust-method |
| Update a Biclust or BiBitWorkflow Object with a new Noise Level | UpdateBiclust_RowNoise |
