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]

# 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-1.19.2(bioc 3.24)enhancerHomologSearch-1.18.0(bioc 3.23)

sequencing generegulation alignment cpp

4.88 score 2 scripts 303 downloads 23 exports 91 dependencies

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

Target	Result	Time
bioc-checks	NOTE	580
linux-devel-arm64	ERROR	791
linux-devel-x86_64	ERROR	960
source / vignettes	OK	1083
linux-release-arm64	OK	857
linux-release-x86_64	OK	1004
macos-release-arm64	OK	768
macos-release-x86_64	OK	3137
macos-oldrel-arm64	OK	757
macos-oldrel-x86_64	OK	2340
windows-devel	ERROR	1282
windows-release	OK	1412
windows-oldrel	OK	1440
wasm-release	OK	703

Exports:alignment alignmentOne coerce conservedMotifs distance distance<-Enhancers genome genome<-getENCODEdata getSeq peaks peaks<-query_tfbp queryEncode saveAlignments searchTFBPS seqinfo show shuffle subset subsetByOverlaps tfbp

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cigarillo cli codetools cpp11 crayon curl DBI dbplyr DelayedArray DirichletMultinomial dplyr fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue gtools httr httr2 IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime motifmatchr MultipleAlignment openssl pillar pkgconfig purrr pwalign R6 rappdirs Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo seqLogo snow SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect utf8 vctrs withr XML XVector yaml

enhancerHomologSearch Guide

Introduction | Installation | Step 1, prepare target enhancer sequences. | Step 2, download candidate regions of enhancers from ENCODE by H3K4me1 marks | Step 3, get alignment score for target enhancer and candidate enhancers. | Step 4, filter the candidate regions. | Step 5, alignment for the enhancer and the orthologs | Step 6a, for quick evolution enhancers, check the conserved motifs in the orthologs | Step 6b, for slow evolution enhancers, export the multiple alignments in order. | Session info

Rendered fromenhancerHomologSearch.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Output	alignment
Get alignment scores	alignmentOne
check the conserved motifs in the orthologs	conservedMotifs
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 ENCODE	getENCODEdata
Pre-clustered motifs from human and mouse	motifs
query data from ENCODE by predefined criteria	queryEncode
output alignments	saveAlignments
Transcription Factor Binding Pattern Similarity (TFBPS) search	searchTFBPS
shuffle reads	shuffle