Package: MMDiff2 1.41.0

Gabriele Schweikert

MMDiff2: Statistical Testing for ChIP-Seq data sets

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

Authors:Gabriele Schweikert [cre, aut], David Kuo [aut]

MMDiff2_1.41.0.tar.gz
MMDiff2_1.41.0.zip(r-4.7)MMDiff2_1.41.0.zip(r-4.6)MMDiff2_1.41.0.zip(r-4.5)
MMDiff2_1.41.0.tgz(r-4.6-any)MMDiff2_1.41.0.tgz(r-4.5-any)
MMDiff2_1.41.0.tar.gz(r-4.7-any)MMDiff2_1.41.0.tar.gz(r-4.6-any)
MMDiff2_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MMDiff2/json (API)

# Install 'MMDiff2' in R:

install.packages('MMDiff2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

MMD - DBAmmd Object for Cfp1 example

On BioConductor:MMDiff2-1.41.0(bioc 3.24)MMDiff2-1.40.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipseq differentialpeakcalling sequencing software

3.30 score 1 scripts 24 exports 88 dependencies

Last updated from:12f6051464. Checks:4 WARNING, 4 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	267
linux-devel-x86_64	NOTE	451
source / vignettes	OK	411
linux-release-x86_64	NOTE	511
macos-release-arm64	NOTE	277
macos-oldrel-arm64	NOTE	296
windows-devel	WARNING	374
windows-release	WARNING	376
windows-oldrel	WARNING	373
wasm-release	OK	249

Exports:compDists compHists compPvals Contrast Counts DBAmmd Dists estimateFragmentCenters Genome getPeakReads Hists metaData numPeaks numSamples plotDists plotDISTS4Peak plotPeak Reads Regions reportResults runShinyMMDiff2 Samples setContrast setRegions

Dependencies:abind askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome bslib cachem cigarillo cli codetools commonmark cpp11 crayon curl DelayedArray digest farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable htmltools httpuv httr IRanges isoband jquerylib jsonlite labeling lambda.r later lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel promises R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shiny snow sourcetools SparseArray SummarizedExperiment sys vctrs viridisLite withr XML xtable XVector yaml

An Introduction to the MMDiff2 method

1 Introduction | 2 Quick Start | 3 Analysis Pipeline | 4 Comparison with DiffBind | 5 Setup

Rendered fromMMDiff2.Rnwusingknitr::knitr

Last update: 2016-04-26
Started: 2016-04-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Peaks for Cfp1-data set	Cfp1-Peaks
Compute distances between Peaks	compDists
Compute Peak histograms	compHists
compute p-values	compPvals
Extract data from DBAmmd objects	Contrast,DBAmmd-method Counts,DBAmmd-method DBAmmd-Accessors Dists,DBAmmd-method Genome,DBAmmd-method Hists,DBAmmd-method metaData,DBAmmd-method numPeaks,DBAmmd-method numSamples,DBAmmd-method Reads,DBAmmd-method Regions,DBAmmd-method Samples,DBAmmd-method setContrast,DBAmmd-method setRegions,DBAmmd-method
Class DBAmmd	DBAmmd DBAmmd-class
estimate center of fragments	estimateFragmentCenters
Get reads from indexed bam files for defined regions	getPeakReads
Generics for DBAmmd-Class	Contrast Counts Dists Genome Hists metaData numPeaks numSamples Reads Regions Samples setContrast setRegions
mm9-Genes	mm9-Genes
DBAmmd Object for Cfp1 example	MMD
plotDists	plotDists
plotDISTS4Peak	plotDISTS4Peak
plot Peak	plotPeak
report results	reportResults
Shiny Application for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks	runShinyMMDiff2
Shiny server code for interactive visualization of MMD distances, peak plots, and MMD distances by sample.	server.MMDiff2
ui component for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks	ui.MMDiff2