Package: enhancerHomologSearch 1.18.0

Jianhong Ou

enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

Authors:Jianhong Ou [aut, cre], Valentina Cigliola [dtc], Kenneth Poss [fnd]

enhancerHomologSearch_1.18.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
enhancerHomologSearch/json (API)
NEWS

# Install 'enhancerHomologSearch' in R:
install.packages('enhancerHomologSearch', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jianhong/enhancerhomologsearch/issues

Pkgdown/docs site:https://jianhong.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • motifs - Pre-clustered motifs from human and mouse

On BioConductor:enhancerHomologSearch-1.19.0(bioc 3.24)enhancerHomologSearch-1.18.0(bioc 3.23)

sequencinggeneregulationalignmentcpp

4.65 score 2 scripts 330 downloads 23 exports 89 dependencies

Last updated from:c43232e600 (on RELEASE_3_23). Checks:9 NOTE, 3 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE570
linux-devel-arm64ERROR868
linux-devel-x86_64ERROR978
source / vignettesOK1170
linux-release-arm64NOTE919
linux-release-x86_64NOTE1042
macos-release-arm64NOTE856
macos-release-x86_64NOTE1878
macos-oldrel-arm64NOTE699
macos-oldrel-x86_64NOTE1590
windows-develERROR1355
windows-releaseNOTE1705
windows-oldrelNOTE1192
wasm-releaseOK399

Exports:alignmentalignmentOnecoerceconservedMotifsdistancedistance<-Enhancersgenomegenome<-getENCODEdatagetSeqpeakspeaks<-query_tfbpqueryEncodesaveAlignmentssearchTFBPSseqinfoshowshufflesubsetsubsetByOverlapstfbp

Dependencies:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDirichletMultinomialdplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrhttr2IRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimemotifmatchropensslpillarpkgconfigpurrrpwalignR6rappdirsRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselectutf8vctrswithrXMLXVectoryaml

enhancerHomologSearch Guide

Jianhong Ou

Rendered fromenhancerHomologSearch.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2023-10-25
Started: 2021-06-21

Readme and manuals

Help Manual

Help pageTopics
Outputalignment
Get alignment scoresalignmentOne
check the conserved motifs in the orthologsconservedMotifs
Class '"Enhancers"'$,Enhancers-method $<-,Enhancers-method coerce coerce,Enhancers,GRanges-method distance distance,Enhancers,ANY-method distance,Enhancers-method distance<- distance<-,Enhancers,ANY-method distance<-,Enhancers-method Enhancers Enhancers-class genome genome,Enhancers-method genome<- genome<-,Enhancers,BSgenome-method genome<-,Enhancers-method getSeq,Enhancers-method peaks peaks,Enhancers-method peaks<- peaks<-,Enhancers,GRanges-method peaks<-,Enhancers-method query_tfbp query_tfbp,Enhancers,ANY-method query_tfbp,Enhancers-method seqinfo,Enhancers-method show,Enhancers-method subset,Enhancers-method subsetByOverlaps,Enhancers,ANY-method subsetByOverlpas,Enhancers-method tfbp tfbp,Enhancers,ANY-method tfbp,Enhancers-method
Download enhancer sequences from ENCODEgetENCODEdata
Pre-clustered motifs from human and mousemotifs
query data from ENCODE by predefined criteriaqueryEncode
output alignmentssaveAlignments
Transcription Factor Binding Pattern Similarity (TFBPS) searchsearchTFBPS
shuffle readsshuffle