Package: enhancerHomologSearch 1.19.2

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_1.19.2.tar.gz
enhancerHomologSearch_1.19.2.zip(r-4.7)enhancerHomologSearch_1.19.2.zip(r-4.6)enhancerHomologSearch_1.19.2.zip(r-4.5)
enhancerHomologSearch_1.19.2.tgz(r-4.6-x86_64)enhancerHomologSearch_1.19.2.tgz(r-4.6-arm64)enhancerHomologSearch_1.19.2.tgz(r-4.5-x86_64)enhancerHomologSearch_1.19.2.tgz(r-4.5-arm64)
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enhancerHomologSearch_1.19.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
enhancerHomologSearch/json (API)
NEWS

# Install 'enhancerHomologSearch' in R:
install.packages('enhancerHomologSearch', repos = c('https://bioc.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

4.88 score 2 scripts 303 downloads 23 exports 91 dependencies

Last updated from:0369241385. Checks:1 NOTE, 3 ERROR, 10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE560
linux-devel-arm64ERROR829
linux-devel-x86_64ERROR999
source / vignettesOK1134
linux-release-arm64OK911
linux-release-x86_64OK1066
macos-release-arm64OK943
macos-release-x86_64OK1519
macos-oldrel-arm64OK664
macos-oldrel-x86_64OK1500
windows-develERROR1359
windows-releaseOK1279
windows-oldrelOK1176
wasm-releaseOK635

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

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDirichletMultinomialdplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrhttr2IRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimemotifmatchrMultipleAlignmentopensslpillarpkgconfigpurrrpwalignR6rappdirsRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselectutf8vctrswithrXMLXVectoryaml

enhancerHomologSearch Guide

Jianhong Ou

Rendered fromenhancerHomologSearch.Rmdusingknitr::rmarkdownon Jun 08 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