Single restriction fragment | Longer bait regions
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-4.7-any)chicane_0.1.8.zip(r-4.6-any)chicane_0.1.8.zip(r-4.5-any)
chicane_0.1.8.tgz(r-4.6-any)chicane_0.1.8.tgz(r-4.5-any)
chicane_0.1.8.tar.gz(r-4.7-any)chicane_0.1.8.tar.gz(r-4.6-any)
chicane_0.1.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
chicane/json (API)
| # Install 'chicane' in R: |
| install.packages('chicane', repos = c('https://syedhaider5.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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 from:a6c7fced08. Checks:1 WARNING, 2 OK, 6 NOTE. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 633 | ||
| source / vignettes | OK | 1160 | ||
| linux-release | NOTE | 888 | ||
| macos-release | NOTE | 1188 | ||
| macos-oldrel | NOTE | 1030 | ||
| windows-devel | NOTE | 565 | ||
| windows-release | NOTE | 555 | ||
| windows-oldrel | NOTE | 734 | ||
| wasm-release | OK | 518 |
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.tabledescdiffobjdigestdoParallelevaluatefastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgamlssgamlss.datagamlss.distgamlss.trgluehighrhtmltoolsiteratorsjquerylibjsonliteknitrlambda.rlatticelifecyclemagrittrMASSMatrixmemoisemimenlmeotelpkgbuildpkgloadpraiseprocessxpsR.methodsS3R.ooR.utilsR6rappdirsrlangrmarkdownrprojrootsasssurvivaltestthattinytexVennDiagramwaldowithrxfunyaml
Visualising Interactions
Last update: 2021-11-06
Started: 2018-08-30
Getting Started with Capture Hi-C Analysis Engine
Background | Quickstart | Pre-processing data | Statistical model | Distribution of the counts | Negative binomial | Poisson | Truncated negative binomial | Truncated poisson | Adjusting for covariates | Custom covariates | Filtering baits and targets | Merging biological replicates | Assessing model fits | Setting distance bins | Multiple testing correction | Interpretation of interaction peaks | Annotation with bedtools | Visualising interaction peaks in WashU Epigenome Browser | Locus plots | Background Interactions | Example Workflow (T-47D breast cancer cell line) | Session Info | Acknowledgements | References
Last update: 2021-07-25
Started: 2021-01-13
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 |