Package: DAMEfinder 1.19.0

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_1.19.0.tar.gz
DAMEfinder_1.19.0.zip(r-4.5)DAMEfinder_1.19.0.zip(r-4.4)DAMEfinder_1.19.0.zip(r-4.3)
DAMEfinder_1.19.0.tgz(r-4.4-any)DAMEfinder_1.19.0.tgz(r-4.3-any)
DAMEfinder_1.19.0.tar.gz(r-4.5-noble)DAMEfinder_1.19.0.tar.gz(r-4.4-noble)
DAMEfinder_1.19.0.tgz(r-4.4-emscripten)DAMEfinder_1.19.0.tgz(r-4.3-emscripten)
DAMEfinder.pdf |DAMEfinder.html✨
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-1.17.0(bioc 3.20)DAMEfinder-1.16.0(bioc 3.19)

dnamethylation differentialmethylation coverage

5.70 score 10 stars 9 scripts 257 downloads 11 exports 112 dependencies

Last updated 23 days agofrom:faefd56f5a. Checks:OK: 2 NOTE: 3 ERROR: 2. Indexed: yes.

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

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

DAMEfinder Workflow

Stephany Orjuela, Dania Machlab, Mark Robinson

Rendered fromDAMEfinder_workflow.Rmdusingknitr::rmarkdownon Oct 30 2024.

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