Introduction | What is allele-specific methylation? | Overview | Why SNP-based? | Why tuple-based? | Installation | Get bam files | SNP-based (aka slow-mode) | Example Workflow | Obtain allele-based methylation calls | Summarize methylation calls across samples | Find DAMEs | tuple-based (aka fast-mode) | Run Methtuple on bam files | Read methtuple files | Calculate ASM Score | Visualization | DAME tracks | Methyl-circle plot | MDS plot | Session Info | References
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
DAMEfinder/json (API)
| # 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)
dnamethylationdifferentialmethylationcoverage
Last updated from:49423a64ec. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 248 | ||
| linux-devel-x86_64 | NOTE | 506 | ||
| source / vignettes | OK | 360 | ||
| linux-release-x86_64 | NOTE | 466 | ||
| macos-release-arm64 | NOTE | 237 | ||
| macos-oldrel-arm64 | NOTE | 269 | ||
| windows-devel | NOTE | 338 | ||
| windows-release | NOTE | 352 | ||
| windows-oldrel | NOTE | 369 | ||
| wasm-release | OK | 246 |
Exports:calc_asmcalc_derivedasmdame_trackdame_track_meanextract_bamsfind_damesget_tstatsmethyl_circle_plotmethyl_circle_plotCpGmethyl_MDS_plotread_tuples
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebumphuntercachemcigarilloclicliprcodetoolscowplotcpp11crayoncurlDBIDelayedArraydigestdoRNGfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrpngprettyunitsprogressR6RColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyselecttzdbutf8VariantAnnotationvctrsviridisLitevroomwithrXMLXVectoryaml
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 |
