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monaLisa

binned motif enrichment analysis and visualisation

https://github.com/fmicompbio/monalisa

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
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    1 of 8 committers (12.5%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (12.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics functional-similarity gene gene-sets pathway-analysis similarity similarity-measurement mirror
Last synced: 7 months ago · JSON representation

Repository

binned motif enrichment analysis and visualisation

Basic Info
Statistics
  • Stars: 41
  • Watchers: 7
  • Forks: 7
  • Open Issues: 8
  • Releases: 0
Created almost 8 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

README.md

monaLisa


monaLisa: MOtif aNAlysis with Lisa


Overview

monaLisa was inspired by her father Homer to look for enriched motifs in sets (bins) of genomic regions, compared to all other regions ("binned motif enrichment analysis").

It uses known motifs representing transcription factor binding preferences, for example for the JASPAR2020 Bioconductor package. The regions are for example promoters or accessible regions, which are grouped into bins according to a numerical value assigned to each region, such as change of expression or accessibility. The goal of the analysis is to identify transcription factors that are associated to that numerical value and thus candidates to be drivers in the underlying biological process.

In addition to the "binned motif enrichment analysis", monaLisa can also be used to address the above question using stability selection (a form of linear regression), or to look for motif matches in sequences.

Current contributors include:

News

Citation

To cite monaLisa please use the publication found here or see citation("monaLisa").

Installation

monaLisa can be installed from Bioconductor via the BiocManager package:

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("monaLisa") ```

Functionality

Here is a minimal example to run a monaLisa analysis:

``` library(monaLisa)

mcparams <- BiocParallel::MulticoreParam(10L) se <- calcBinnedMotifEnrR(seqs = seqs, # DNAStringSet (e.g. peak sequences) bins = bins, # factor that groups 'seqs' pwmL = pwms, # PWMatrixList (know motifs) BPPARAM = mcparams, min.score = 10, verbose = TRUE) ```

The return value se is a SummarizedExperiment with motifs in rows and bins in columns, and multiple assays with significance and magnitude of the enrichments.

The inputs for calcBinnedMotifEnrR can be easily obtained using other Bioconductor packages:
```

get sequences ('lmrs' is a GRanges object)

library(Biostrings) library(BSgenome.Mmusculus.UCSC.mm10) seqs <- getSeq(BSgenome.Mmusculus.UCSC.mm10, lmrs)

bin sequences ('deltaMeth' is a numerical vector)

bins <- monaLisa::bin(x = deltaMeth, binmode = "equalN", nElement = 800)

obtain known motifs from Jaspar

library(JASPAR2020) library(TFBSTools) pwms <- getMatrixSet(JASPAR2020, list(matrixtype = "PWM", tax_group = "vertebrates")) ```

The results can be conveniently visualized: plotBinDensity(deltaMeth, bins, legendPosition = "none") + labs(x = "Methylation difference") binning

plotMotifHeatmaps(se, cluster = TRUE, which.plots = c("enr", "FDR"), show_seqlogo = TRUE) heatmaps

Github Actions (multiple OS): R build status Codecov.io coverage status <!-- badges: end -->

Owner

  • Login: fmicompbio
  • Kind: user

GitHub Events

Total
  • Issues event: 5
  • Watch event: 5
  • Delete event: 4
  • Issue comment event: 12
  • Push event: 50
  • Pull request review comment event: 40
  • Pull request review event: 33
  • Pull request event: 11
  • Fork event: 1
  • Create event: 6
Last Year
  • Issues event: 5
  • Watch event: 5
  • Delete event: 4
  • Issue comment event: 12
  • Push event: 50
  • Pull request review comment event: 40
  • Pull request review event: 33
  • Pull request event: 11
  • Fork event: 1
  • Create event: 6

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,010
  • Total Committers: 8
  • Avg Commits per committer: 126.25
  • Development Distribution Score (DDS): 0.385
Past Year
  • Commits: 7
  • Committers: 3
  • Avg Commits per committer: 2.333
  • Development Distribution Score (DDS): 0.571
Top Committers
Name Email Commits
mbstadler s****l@g****m 621
machlabd d****b@g****m 230
Charlotte Soneson c****n@g****m 111
burgerlu l****r@f****h 37
Nitesh Turaga n****a@g****m 4
burgerlu b****u@x****h 3
J Wokaty j****y@s****u 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 xenon4.fmi.ch: 1 fmi.ch: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 49
  • Total pull requests: 44
  • Average time to close issues: 5 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 17
  • Total pull request authors: 4
  • Average comments per issue: 2.06
  • Average comments per pull request: 1.52
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 14
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 6 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.75
  • Average comments per pull request: 1.79
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • LukasBurger (14)
  • mbstadler (12)
  • csoneson (4)
  • machlabd (4)
  • olechnwin (2)
  • cxtaslim (2)
  • NathanHarmston (1)
  • leezx (1)
  • Smartmandm (1)
  • nsoriano2 (1)
  • IStevant (1)
  • zhezhenwang (1)
  • stianale (1)
  • lengfei5 (1)
  • xflicsu (1)
Pull Request Authors
  • csoneson (19)
  • mbstadler (18)
  • machlabd (9)
  • danymukesha (2)
Top Labels
Issue Labels
enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 12,785 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: monaLisa

Binned Motif Enrichment Analysis and Visualization

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 12,785 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 6.0%
Forks count: 10.0%
Average: 19.5%
Downloads: 81.3%
Maintainers (1)
michael.stadler@fmi.ch
Last synced: 8 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • BSgenome * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • ComplexHeatmap >= 2.11.1 imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • TFBSTools * imports
  • XVector * imports
  • circlize * imports
  • glmnet * imports
  • grDevices * imports
  • graphics * imports
  • grid * imports
  • methods * imports
  • stabs * imports
  • stats * imports
  • tools * imports
  • utils * imports
  • vioplot * imports
  • BSgenome.Mmusculus.UCSC.mm10 * suggests
  • BiocStyle * suggests
  • JASPAR2020 * suggests
  • TxDb.Mmusculus.UCSC.mm10.knownGene * suggests
  • gridExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests