Package: bumphunter 1.49.0

Tamilselvi Guharaj

bumphunter: Bump Hunter

Tools for finding bumps in genomic data

Authors:Rafael A. Irizarry [aut], Martin Aryee [aut], Kasper Daniel Hansen [aut], Hector Corrada Bravo [aut], Shan Andrews [ctb], Andrew E. Jaffe [ctb], Harris Jaffee [ctb], Leonardo Collado-Torres [ctb], Tamilselvi Guharaj [cre]

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

# Install 'bumphunter' in R:

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

Bug tracker:https://github.com/rafalab/bumphunter/issues

Datasets:

TT - Example data

On BioConductor:bumphunter-1.49.0(bioc 3.21)bumphunter-1.48.0(bioc 3.20)

dnamethylation epigenetics infrastructure multiplecomparison immunooncology

11.74 score 16 stars 42 packages 210 scripts 4.7k downloads 46 mentions 14 exports 76 dependencies

Last updated 4 months agofrom:28669ca9b4. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 17 2025
R-4.5-win	NOTE	Feb 17 2025
R-4.5-mac	NOTE	Feb 17 2025
R-4.5-linux	NOTE	Feb 17 2025
R-4.4-win	NOTE	Feb 17 2025
R-4.4-mac	NOTE	Feb 17 2025
R-4.3-win	NOTE	Feb 17 2025
R-4.3-mac	NOTE	Feb 17 2025

Exports:annotateNearest annotateTranscripts boundedClusterMaker bumphunter bumphunterEngine clusterMaker dummyData getSegments locfitByCluster loessByCluster matchGenes regionFinder runmedByCluster smoother

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI DelayedArray digest doRNG fastmap foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray statmod SummarizedExperiment sys UCSC.utils vctrs XML XVector yaml

The bumphunter user's guide

Rendered frombumphunter.Rnwusingutils::Sweaveon Feb 17 2025.

Last update: 2018-11-02
Started: 2014-05-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate the results of nearest	annotateNearest
Annotate transcripts	annotateTranscripts
Bumphunter	bumphunter bumphunter,matrix-method bumphunter-methods bumphunterEngine print.bumps
Make clusters of genomic locations based on distance	boundedClusterMaker clusterMaker
Generate dummy data for use with bumphunter functions	dummyData
Segment a vector into positive, zero, and negative regions	getSegments
Apply local regression smoothing to values within each spatially-defined cluster.	locfitByCluster
Apply loess smoothing to values within each spatially-defined cluster.	loessByCluster
Find and annotate closest genes to genomic regions	matchGenes
Find non-zero regions in vector	regionFinder
Apply running median smoothing to values within each spatially-defined cluster	runmedByCluster
Smooth genomic profiles	smoother
Example data	TT