Package: DAMEfinder 1.25.0

Stephany Orjuela

DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

'DAMEfinder' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.

Authors:Stephany Orjuela [aut, cre], Dania Machlab [aut], Mark Robinson [aut]

DAMEfinder_1.25.0.tar.gz
DAMEfinder_1.25.0.zip(r-4.7)DAMEfinder_1.25.0.zip(r-4.6)DAMEfinder_1.25.0.zip(r-4.5)
DAMEfinder_1.25.0.tgz(r-4.6-any)DAMEfinder_1.25.0.tgz(r-4.5-any)
DAMEfinder_1.25.0.tar.gz(r-4.7-any)DAMEfinder_1.25.0.tar.gz(r-4.6-any)
DAMEfinder_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DAMEfinder/json (API)
NEWS

# Install 'DAMEfinder' in R:

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

Bug tracker:https://github.com/markrobinsonuzh/damefinder/issues

Datasets:

extractbams_output - Extract_bams() output.
readtuples_output - Read_tuples() output.

On BioConductor:DAMEfinder-1.25.0(bioc 3.24)DAMEfinder-1.24.0(bioc 3.23)

dnamethylation differentialmethylation coverage

6.00 score 10 stars 10 scripts 472 downloads 1 mentions 11 exports 106 dependencies

Last updated from:49423a64ec. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	218
linux-devel-x86_64	NOTE	463
source / vignettes	OK	412
linux-release-x86_64	NOTE	470
macos-release-arm64	NOTE	302
macos-oldrel-arm64	NOTE	255
windows-devel	NOTE	462
windows-release	NOTE	366
windows-oldrel	NOTE	373
wasm-release	OK	229

Exports:calc_asm calc_derivedasm dame_track dame_track_mean extract_bams find_dames get_tstats methyl_circle_plot methyl_circle_plotCpG methyl_MDS_plot read_tuples

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bumphunter cachem cigarillo cli clipr codetools cowplot cpp11 crayon curl DBI DelayedArray digest doRNG farver fastmap foreach formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyr png prettyunits progress R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyselect tzdb utf8 VariantAnnotation vctrs viridisLite vroom withr XML XVector yaml

DAMEfinder Workflow

Stephany Orjuela, Dania Machlab, Mark Robinson

Rendered fromDAMEfinder_workflow.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2023-04-04
Started: 2017-04-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate ASM Score	calc_asm
Calculate SNP-based ASM	calc_derivedasm
Calculate the log odds ratio	calc_logodds
Calculate score	calc_score
Calculate Weight for ASM Score	calc_weight
Plot score tracks	dame_track
Plot means per group of score tracks.	dame_track_mean
DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.	DAMEfinder
Detect allele-specific methylation from a bam file	extract_bams
extract_bams() output.	extractbams_output
Find DAMEs	find_dames
Get t-Statistics	get_tstats
Draw methylation circle plot	methyl_circle_plot
Draw methylation circle plot without SNP	methyl_circle_plotCpG
Multidimensional scaling plot of distances between methylation proportions (beta values)	methyl_MDS_plot
Get Modulus Square Root	modulus_sqrt
Read in list of methtuple files	read_tuples
read_tuples() output.	readtuples_output