Overview | Installation | Requirements | Input files | Running the full pipeline | Step 1 — prepare_cpg_snp_input() | Step 2 — extract_bam_regions() | Step 3 — ASM() | Output files
Package: ImprintCapASM 0.1.1
Subham Saha
ImprintCapASM: Allele-Specific Methylation Analysis for Imprinted DMR Diagnostics
Provides functions for SNP-phased allele-specific methylation (ASM) analysis across the 41 canonical human imprinted differentially methylated regions (DMRs). Reads are assigned to REF or ALT alleles based on bisulfite-aware SNP detection, enabling diagnosis of imprinting disorders from whole-genome bisulfite sequencing data. <https://github.com/19-saha/ImprintCapASM>.
Authors:
ImprintCapASM_0.1.1.tar.gz
ImprintCapASM_0.1.1.tar.gz(r-4.7-any)ImprintCapASM_0.1.1.tar.gz(r-4.6-any)
ImprintCapASM_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ImprintCapASM/json (API)
| # Install 'ImprintCapASM' in R: |
| install.packages('ImprintCapASM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/19-saha/imprintcapasm/issues
Last updated from:af05a11d2a. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 279 | ||
| source / vignettes | OK | 230 | ||
| linux-release-x86_64 | OK | 236 | ||
| wasm-release | OK | 165 |
Exports:ASMextract_bam_regionsprepare_cpg_snp_inputrun_pipeline
Dependencies:apeBHBiocGenericsBiocParallelBiostringsbitopscellrangercliclustercodetoolscpp11crayondata.tabledigestdplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehmsIRangesisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigprettyunitsprogressR6RColorBrewerRcppreadxlrematchRhtslibrlangRsamtoolsS4VectorsS7scalesSeqinfosnowstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithrwritexlXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Run Allele-Specific Methylation Analysis | ASM |
| Extract BAM Regions Around SNP Windows | extract_bam_regions |
| Prepare CpG-SNP Input Table | prepare_cpg_snp_input |
| Run the Full ImprintCapASM Pipeline | run_pipeline |