Package: nullranges 1.13.0
Michael Love
nullranges: Generation of null ranges via bootstrapping or covariate matching
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
Authors:
nullranges_1.13.0.tar.gz
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nullranges.pdf |nullranges.html✨
nullranges/json (API)
NEWS
| # Install 'nullranges' in R: |
| install.packages('nullranges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nullranges/nullranges/issues
Pkgdown:https://nullranges.github.io
On BioConductor:nullranges-1.13.0(bioc 3.21)nullranges-1.12.0(bioc 3.20)
visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics
Last updated 2 months agofrom:8b245866f4. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 24 2024 |
| R-4.5-win | NOTE | Nov 24 2024 |
| R-4.5-linux | NOTE | Nov 24 2024 |
| R-4.4-win | NOTE | Nov 24 2024 |
| R-4.4-mac | NOTE | Nov 24 2024 |
| R-4.3-win | OK | Nov 24 2024 |
| R-4.3-mac | OK | Nov 24 2024 |
Exports:bootRangesBootRangescombnCovcovariatesfocalindicesmakeExampleMatchedDataSetmatchedMatchedmatchedDataMatchedDataFrameMatchedGInteractionsMatchedGRangesmatchRangesmethodoneRegionSegmentoverviewplotCovariateplotPropensityplotSegmentpoolreduceSegmentsegmentDensityshowunmatchedwithReplacement
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggridgesgluegtablehmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrangesprettyunitsprogressR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
Introduction to nullranges
Rendered fromnullranges.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2022-12-30
Started: 2020-12-22
Introduction to bootRanges
Rendered frombootRanges.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2023-08-21
Started: 2023-01-03
Introduction to matchRanges
Rendered frommatchRanges.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2023-06-23
Started: 2023-01-13
Matching case study I: CTCF occupancy
Rendered frommatching_granges.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2023-08-02
Started: 2021-06-01
Matching case study II: CTCF orientation
Rendered frommatching_ginteractions.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2023-08-02
Started: 2021-06-01
Creating a pool set for matchRanges
Rendered frommatching_pool_set.Rmdusingknitr::rmarkdownon Nov 24 2024.Last update: 2023-01-13
Started: 2022-12-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Block bootstrap for genomic ranges | bootRanges |
| BootRanges object | BootRanges BootRanges-class |
| Function for creating combinations of covariates | combnCov combnCov,character-method |
| Get covariates from a Matched object | covariates covariates,Matched-method |
| Get focal set from a Matched object | focal focal,MDF_OR_MGR_OR_MGI-method |
| Get indices of matched set | indices indices,Matched-method |
| Function for generating an example matchRanges or Matched dataset | makeExampleMatchedDataSet makeExampleMatchedDataSet,character_OR_missing,logical_OR_missing,character_OR_missing,logical_OR_missing-method |
| Get matched set from a Matched object | matched matched,MDF_OR_MGR_OR_MGI-method |
| Matched objects | Matched Matched-class |
| Get matched data from a Matched object | matchedData matchedData,Matched-method |
| MatchedDataFrame objects | MatchedDataFrame MatchedDataFrame-class |
| MatchedGInteractions objects | MatchedGInteractions MatchedGInteractions-class |
| MatchedGRanges objects | MatchedGRanges MatchedGRanges-class |
| Generate a covariate-matched control set of ranges | matchRanges matchRanges,DF_OR_df_OR_dt,DF_OR_df_OR_dt,formula,character_OR_missing,logical_OR_missing-method matchRanges,GInteractions,GInteractions,formula,character_OR_missing,logical_OR_missing-method matchRanges,GRanges,GRanges,formula,character_OR_missing,logical_OR_missing-method |
| Get matching method used for Matched object | method method,Matched-method |
| Segmentation based on one region | oneRegionSegment |
| Overview of matching quality | overview overview,Matched,numeric_OR_missing-method |
| Covariate plotting for Matched objects | plotCovariate plotCovariate,Matched,character_OR_missing,character_OR_missing,character_OR_missing,character_OR_missing-method |
| Propensity score plotting for Matched objects | plotPropensity plotPropensity,Matched,character_OR_missing,character_OR_missing,character_OR_missing-method |
| Plot genome segmentation | plotSegment |
| Get pool set from a Matched object | pool pool,MDF_OR_MGR_OR_MGI-method |
| Combine nearby regions with same state | reduceSegment |
| Genome segmentation based on feature density | segmentDensity |
| Get unmatched set from a Matched object | unmatched unmatched,MDF_OR_MGR_OR_MGI-method |
| Get replace method | withReplacement withReplacement,Matched-method |
