Package: extraChIPs 1.11.0
Stevie Pederson
extraChIPs: Additional functions for working with ChIP-Seq data
This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.
Authors:
extraChIPs_1.11.0.tar.gz
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extraChIPs_1.11.0.tgz(r-4.4-x86_64)extraChIPs_1.11.0.tgz(r-4.4-arm64)extraChIPs_1.11.0.tgz(r-4.3-x86_64)extraChIPs_1.11.0.tgz(r-4.3-arm64)
extraChIPs_1.11.0.tar.gz(r-4.5-noble)extraChIPs_1.11.0.tar.gz(r-4.4-noble)
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extraChIPs.pdf |extraChIPs.html✨
extraChIPs/json (API)
NEWS
| # Install 'extraChIPs' in R: |
| install.packages('extraChIPs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/smped/extrachips/issues
- ex_genes - Datasets for an example region
- ex_hic - Datasets for an example region
- ex_prom - Datasets for an example region
- ex_trans - Datasets for an example region
- grch37.cytobands - Cytogenetic bands
- grch38.cytobands - Cytogenetic bands
- peaks - Datasets for the Fixed-Width Vignette
- se - Datasets for the Fixed-Width Vignette
On BioConductor:extraChIPs-1.9.6(bioc 3.20)extraChIPs-1.8.5(bioc 3.19)
Last updated 23 days agofrom:f411e4cf67. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:addDiffStatusbestOverlapcentrePeakschopMCcollapseGenescolToRangesdefineRegionsdefineSeqinfodistinctMCdualFilterfitAssayDiffgetProfileDatagrlToSEimportPeaksintersectMCmakeConsensusmapByFeaturemapGrlColsmergeByColmergeByHMPmergeBySigpartitionRangesplotAssayDensitiesplotAssayHeatmapplotAssayPCAplotAssayRleplotGrlColplotHFGCplotOverlapsplotPairwiseplotPieplotProfileHeatmapplotSplitDonutpropOverlapreduceMCsetdiffMCstitchRangesunionMCvoomWeightsFromCPM
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbroomBSgenomebslibcachemcheckmatecliclustercodetoolscolorspaceComplexUpsetcpp11crayoncsawcurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyredgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggforceggplot2ggrepelggsidegluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetapodmgcvmimemunsellnlmennetopensslpatchworkpillarpkgconfigplogrpngpolyclipprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttinytextweenrUCSC.utilsutf8VariantAnnotationvctrsVennDiagramviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
extraChIPs: Differential Signal Using Fixed-Width Windows
Rendered fromdifferential_signal_fixed.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2023-10-09
Started: 2023-06-20
extraChIPs: Differential Signal Using Sliding Windows
Rendered fromdifferential_signal_sliding.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-07-22
Started: 2023-06-20
extraChIPs: Range-Based operations
Rendered fromrange_based_functions.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2023-04-13
Started: 2022-03-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add a status column | addDiffStatus addDiffStatus,data.frame-method addDiffStatus,DataFrame-method addDiffStatus,GRanges-method addDiffStatus,GRangesList-method addDiffStatus,SummarizedExperiment-method |
| Convert to a tibble | as_tibble as_tibble.DataFrame as_tibble.GenomicRanges as_tibble.GInteractions as_tibble.Seqinfo as_tibble.SummarizedExperiment as_tibble.TopTags |
| Find the best overlap between GRanges | bestOverlap bestOverlap,GRanges,GRanges-method bestOverlap,GRanges,GRangesList-method |
| Re-estimate peak centres from coverage | centrePeaks centrePeaks,GRanges,BamFile-method centrePeaks,GRanges,BamFileList-method centrePeaks,GRanges,BigWigFile-method centrePeaks,GRanges,BigWigFileList-method centrePeaks,GRanges,character-method |
| Keep unique ranges and collapse mcols | chopMC |
| Collapse a vector of gene names | collapseGenes |
| Coerce a column to a GRanges object | colToRanges colToRanges,data.frame-method colToRanges,DataFrame-method colToRanges,GRanges-method |
| Cytogenetic bands | cytobands grch37.cytobands grch38.cytobands |
| Define Genomic Regions Based on Gene Annotations | defineRegions |
| Use package data to define a Seqinfo object | defineSeqinfo |
| Keep distinct ranges and mcols | distinctMC |
| Apply two filters to sliding windows | dualFilter |
| Datasets for an example region | ex_datasets ex_genes ex_hic ex_prom ex_trans |
| Detect Differential ChIP Signal | fitAssayDiff fitAssayDiff,SummarizedExperiment-method |
| Datasets for the Fixed-Width Vignette | fixed_width_datasets peaks se |
| Get Profile Data surrounding specified ranges | getProfileData getProfileData,BigWigFile,GenomicRanges-method getProfileData,BigWigFileList,GenomicRanges-method getProfileData,character,GenomicRanges-method |
| Set columns from a GRangesList as Assays in a SummarizedExperiment | grlToSE grlToSE,GRangesList-method |
| Import peaks | importPeaks |
| Make a set of consensus peaks | makeConsensus |
| Map Genomic Ranges to genes using defined features | mapByFeature |
| Collapse a GRangesList adding multiple columns from each element | mapGrlCols |
| Merge sliding windows using a specified column | mergeByCol mergeByCol,GenomicRanges-method mergeByCol,RangedSummarizedExperiment-method |
| Merge Sliding Windows using the Harmonic Mean P | mergeByHMP mergeByHMP,GenomicRanges-method mergeByHMP,RangedSummarizedExperiment-method |
| Merge overlapping ranges based on p-values | mergeBySig mergeBySig,GenomicRanges-method mergeBySig,RangedSummarizedExperiment-method |
| Partition a set of Genomic Ranges | partitionRanges partitionRanges,GRanges,GRanges-method |
| Plot Densities for any assay within a SummarizedExperiment | plotAssayDensities plotAssayDensities,SummarizedExperiment-method |
| Draw a heatmap from a single SummarizedExperiment assay | plotAssayHeatmap plotAssayHeatmap,SummarizedExperiment-method |
| Plot PCA For any assay within a SummarizedExperiment | plotAssayPCA plotAssayPCA,SummarizedExperiment-method |
| Plot RLE for a given assay within a SummarizedExperiment | plotAssayRle plotAssayRle,SummarizedExperiment-method |
| Draw a plot from a GRangesList column | plotGrlCol |
| Plot a Genomic Region showing HiC, Features, Genes and Coverage | plotHFGC |
| Plot Overlaps Between List Elements | plotOverlaps plotOverlaps,GRangesList-method plotOverlaps,list-method |
| Plot Pairwise Values from a GRangeList | plotPairwise |
| Draw Pie Graphs based on one or more columns | plotPie plotPie,data.frame-method plotPie,DataFrame-method plotPie,GRanges-method |
| Draw a coverage Profile Heatmap | plotProfileHeatmap plotProfileHeatmap,GenomicRanges-method plotProfileHeatmap,GenomicRangesList-method |
| Draw Two-Level Donut Charts | plotSplitDonut plotSplitDonut,data.frame-method plotSplitDonut,DataFrame-method plotSplitDonut,GRanges-method |
| Find the proportions of an overlapping range | propOverlap propOverlap,GRanges,GRanges-method |
| Reduce ranges retaining mcols | reduceMC |
| Perform set operations retaining mcols | intersectMC intersectMC,GRanges,GRanges-method setdiffMC setdiffMC,GRanges,GRanges-method setoptsMC unionMC unionMC,GRanges,GRanges-method |
| Stitch Ranges within a given distance | stitchRanges |
| Estimate voom precision weights directly From CPM values | voomWeightsFromCPM |
