Package: Motif2Site 1.11.0

Peyman Zarrineh

Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.

Authors:Peyman Zarrineh [cre, aut]

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Motif2Site.pdf |Motif2Site.html✨
Motif2Site/json (API)
NEWS

# Install 'Motif2Site' in R:

install.packages('Motif2Site', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/manchesterbioinference/motif2site/issues

On BioConductor:Motif2Site-1.9.0(bioc 3.20)Motif2Site-1.8.0(bioc 3.19)

software sequencing chipseq differentialpeakcalling epigenetics sequencematching

4.00 score 3 scripts 134 downloads 7 exports 116 dependencies

Last updated 23 days agofrom:9d1afd0147. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:Bed2Granges compareBedFiless2UserProvidedRegions compareMotifs2UserProvidedRegions DetectBindingSitesBed DetectBindingSitesMotif pairwisDifferential recenterBindingSitesAcrossExperiments

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome bslib cachem cli codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dplyr edgeR evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite kernlab knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime mixtools munsell nlme openssl pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools rtracklayer S4Arrays S4Vectors sass scales segmented snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zlibbioc

'Motif2Site': an R package to detect binding sites from ChIP-seq and recenter them

Peyman Zarrineh

Rendered fromMotif2Site.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-02-10
Started: 2021-10-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Read a bed file as Genomic Ranges	Bed2Granges
Combine all IP and Input count table files	combine2Table
Combine motif bed files into a combined ranges	combineMotifFiles
Combine count Table and statistics table	combineTestResults
Compare a set of bed files to a user provided regions set	compareBedFiless2UserProvidedRegions
Compare a set of bed files to a provided regions set	CompareBeds2GivenRegions
Comparison motifs locations to a given regions set	CompareMotifs2GivenRegions
Compare a set of motifs to a user provided regions set	compareMotifs2UserProvidedRegions
compute fold enrichment values for an experiment	computeFoldEnrichment
Synthetic datasets used in the package	data
Decompose binding signal among accepted motifs	decomposeBindingSignal
Delete a vector of files	DeleteMultipleFiles
build heurisitc distribution around the binding sites	deriveHeuristicBindingDistribution
Detect binding sites from motif	DetectBindingSites
Detect binding sites from bed motif input	DetectBindingSitesBed
Detect binding sites from sequence motif sequence and mismatchNumber	DetectBindingSitesMotif
FDR cut-off detection Benjamini Hochberg method	DetectFdrCutoffBH
Find motif instances with a certain mismatch number	findMotifs
Fit a kernel density distribution to the obersever heuristic distribution	fitKernelDensity
Convert bam and bed files to 1 nucleotide bed	generate1ntBedAlignment
Detect and Recenter binding sites from ChIP-seq experiments	Motif2Site
Model IP and Input count values with negative Binomal	motifBindingNegativeBinomialCount
count short reads related to each motif for a given ChIPseq file	motifChipCount
count short reads around motifs for all ChIP-seq experiments	motifCount
Process count data and perform negative binomial test	motifTablePreProcess
Negative binomial test of binding using all replicates	NegativeBinomialTestWithReplicate
Detect differential motifs	pairwisDifferential
Suppress messages generated by in external package	quiet
Combine binding sites across experiments	recenterBindingSitesAcrossExperiments
Remove non-bell shpape motifs prior to binding signal decomposition	removeNonBellShapedMotifs
Returns the motif with the highest count	strongestMotif