Package: chicane 0.1.8
chicane: Capture Hi-C Analysis Engine
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Authors:
chicane_0.1.8.tar.gz
chicane_0.1.8.zip(r-4.5)chicane_0.1.8.zip(r-4.4)chicane_0.1.8.zip(r-4.3)
chicane_0.1.8.tgz(r-4.4-any)chicane_0.1.8.tgz(r-4.3-any)
chicane_0.1.8.tar.gz(r-4.5-noble)chicane_0.1.8.tar.gz(r-4.4-noble)
chicane_0.1.8.tgz(r-4.4-emscripten)chicane_0.1.8.tgz(r-4.3-emscripten)
chicane.pdf |chicane.html✨
chicane/json (API)
NEWS
| # Install 'chicane' in R: |
| install.packages('chicane', repos = c('https://syedhaider5.r-universe.dev', 'https://cloud.r-project.org')) |
- bre80 - Bre80 Cell Line
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:a6c7fced08. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-win | WARNING | Aug 23 2024 |
| R-4.5-linux | WARNING | Aug 23 2024 |
| R-4.4-win | WARNING | Aug 23 2024 |
| R-4.4-mac | WARNING | Aug 23 2024 |
| R-4.3-win | WARNING | Aug 23 2024 |
| R-4.3-mac | WARNING | Aug 23 2024 |
Exports:add.covariatesadd.fragment.coordinatesbedtools.installedcheck.model.numerical.fitchicanecombine.replicatescompare.replicatesconvert.hicup.digest.bedconvert.standard.formatconvert.to.one.basedcreate.locus.plotcreate.modelfit.plotdistance.bindistance.splitfill.in.zeroesfill.in.zerosfilter.fragmentsfit.modelget.combination.countget.componentsget.distanceget.id.componentsget.interaction.idget.trans.countsmultiple.testing.correctprepare.dataread.bedstratified.enrichment.sampletest.enrichment
Dependencies:base64encbedrbriobslibcachemcallrclicodetoolscrayondata.tabledescdiffobjdigestdoParallelevaluatefansifastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgamlssgamlss.datagamlss.distgamlss.trgluehighrhtmltoolsiteratorsjquerylibjsonliteknitrlambda.rlatticelifecyclemagrittrMASSMatrixmemoisemimenlmepillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR.methodsS3R.ooR.utilsR6rappdirsrematch2rlangrmarkdownrprojrootsasssurvivaltestthattibbletinytexutf8vctrsVennDiagramwaldowithrxfunyaml
Getting Started with Capture Hi-C Analysis Engine
Rendered fromGetting_Started.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2021-07-25
Started: 2021-01-13
Visualising Interactions
Rendered fromVisualising_Interactions.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2021-11-06
Started: 2018-08-30
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add.covariates | add.covariates |
| add.fragment.coordinates | add.fragment.coordinates |
| bedtools.installed | bedtools.installed |
| Bre80 Cell Line | bre80 |
| check.model.identifiability | check.model.numerical.fit |
| check.split.data.numerical.fit | check.split.data.numerical.fit |
| chicane | chicane |
| combine.replicates | combine.replicates |
| compare.replicates | compare.replicates |
| convert.bam | convert.bam |
| convert.hicup.digest.bed | convert.hicup.digest.bed |
| convert.standard.format | convert.standard.format |
| convert.to.one.based | convert.to.one.based |
| create.locus.plot | create.locus.plot |
| create.modelfit.plot | create.modelfit.plot |
| distance.bin | distance.bin |
| distance.split | distance.split |
| fill.in.zeros | fill.in.zeroes fill.in.zeros |
| filter.fragments | filter.fragments |
| fit.glm | fit.glm |
| fit.model | fit.model |
| get.combination.count | get.combination.count |
| get.components | get.components |
| get.distance | get.distance |
| get.id.components | get.id.components |
| get.interaction.id | get.interaction.id |
| get.trans.counts | get.trans.counts |
| is.glm.nb.maxiter.warning | is.glm.nb.maxiter.warning |
| check.glm.nb.theta.error | is.glm.nb.theta.error |
| is.glm.nb.theta.warning | is.glm.nb.theta.warning |
| model.rows.sanity.check | model.rows.sanity.check |
| model.try.catch | model.try.catch |
| multiple.testing.correct | multiple.testing.correct |
| prepare.data | prepare.data |
| read.bed | read.bed |
| run.model.fitting | run.model.fitting |
| smart.split | smart.split |
| stratified.enrichment.sample | stratified.enrichment.sample |
| test.enrichment | test.enrichment |
| verify.interaction.data | verify.interaction.data |
