Package: spatzie 1.13.0
Jennifer Hammelman
spatzie: Identification of enriched motif pairs from chromatin interaction data
Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.
Authors:
spatzie_1.13.0.tar.gz
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spatzie.pdf |spatzie.html✨
spatzie/json (API)
NEWS
| # Install 'spatzie' in R: |
| install.packages('spatzie', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- anchor_pair_example_count - Spatzie count correlation data set
- anchor_pair_example_match - Spatzie match association data set
- anchor_pair_example_score - Spatzie score correlation data set
- compare_pairs_example - Compare_motif_pairs example
- filter_pairs_example - Spatzie score correlation filtered data set
- int_data_k562 - K562 Enhancer - Promoter Interactions Data Set
- int_data_mslcl - MSLCL Enhancer - Promoter Interactions Data Set
- int_data_yy1 - Mouse YY1 Enhancer - Promoter Interactions Data Set
- interactions_yy1 - Mouse YY1 Enhancer - Promoter Interactions Data Set
- interactions_yy1_enhancer - Mouse YY1 Enhancer - Promoter Interactions Data Set - YY1 enhancers
- interactions_yy1_ep - Mouse YY1 Enhancer - Promoter Interactions Data Set - YY1 enhancers/promoters
- interactions_yy1_promoter - Mouse YY1 Enhancer - Promoter Interactions Data Set - YY1 promoters
- scan_interactions_example - Interactions scanned for motifs - interactionData object
- scan_interactions_example_filtered - Interactions with motifs filtered for significance - interactionData object
On BioConductor:spatzie-1.13.0(bioc 3.21)spatzie-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhictranscription
Last updated 23 days agofrom:c97feec465. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win | WARNING | Nov 14 2024 |
| R-4.5-linux | WARNING | Nov 14 2024 |
| R-4.4-win | WARNING | Nov 14 2024 |
| R-4.4-mac | WARNING | Nov 14 2024 |
| R-4.3-win | WARNING | Nov 14 2024 |
| R-4.3-mac | WARNING | Nov 14 2024 |
Exports:anchor_pair_enrichcompare_motif_pairsfilter_motifsfilter_pair_motifsfind_ep_coenrichmentget_specific_interactionsplot_motif_occurrencescan_motifs
Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmateclicliprclusterCNErcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestDirichletMultinomialdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2glueGO.dbgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifmatchrmunsellnlmennetopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogressProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
YY1 ChIA-PET motif analysis (single call)
Rendered fromsingle-call.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2022-02-03
Started: 2021-05-20
YY1 ChIA-PET motif analysis (step-by-step)
Rendered fromindividual-steps.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2022-02-03
Started: 2021-05-20
