Package: spatzie 1.18.0
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_1.18.0.tar.gz
spatzie_1.18.0.zip(r-4.7)spatzie_1.18.0.zip(r-4.6)spatzie_1.18.0.zip(r-4.5)
spatzie_1.18.0.tgz(r-4.6-any)spatzie_1.18.0.tgz(r-4.5-any)
spatzie_1.18.0.tar.gz(r-4.7-any)spatzie_1.18.0.tar.gz(r-4.6-any)
spatzie_1.18.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
spatzie/json (API)
NEWS
| # Install 'spatzie' in R: |
| install.packages('spatzie', repos = c('https://bioc-release.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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhictranscription
Last updated from:c15b967076 (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 444 | ||
| linux-devel-x86_64 | ERROR | 702 | ||
| source / vignettes | OK | 456 | ||
| linux-release-x86_64 | ERROR | 645 | ||
| macos-release-arm64 | ERROR | 421 | ||
| macos-oldrel-arm64 | ERROR | 281 | ||
| windows-devel | ERROR | 531 | ||
| windows-release | ERROR | 637 | ||
| windows-oldrel | ERROR | 574 | ||
| wasm-release | OK | 295 |
Exports:anchor_pair_enrichcompare_motif_pairsfilter_motifsfilter_pair_motifsfind_ep_coenrichmentget_specific_interactionsplot_motif_occurrencescan_motifs
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestDirichletMultinomialdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2gluegridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemotifmatchrnnetopensslpillarpkgconfigpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
YY1 ChIA-PET motif analysis (single call)
Rendered fromsingle-call.Rmdusingknitr::rmarkdownon May 28 2026.Last update: 2025-07-23
Started: 2021-05-20
YY1 ChIA-PET motif analysis (step-by-step)
Rendered fromindividual-steps.Rmdusingknitr::rmarkdownon May 28 2026.Last update: 2025-07-23
Started: 2021-05-20
