Package: NanoMethViz 3.3.0
Shian Su
NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
Authors:
NanoMethViz_3.3.0.tar.gz
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NanoMethViz.pdf |NanoMethViz.html✨
NanoMethViz/json (API)
NEWS
| # Install 'NanoMethViz' in R: |
| install.packages('NanoMethViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
The latest version of this package failed to build. Look at thebuild logs for more information.
Bug tracker:https://github.com/shians/nanomethviz/issues
Pkgdown:https://shians.github.io
On BioConductor:NanoMethViz-3.3.0(bioc 3.21)NanoMethViz-3.2.0(bioc 3.20)
softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
Last updated 2 months agofrom:1ee21fe29e. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 25 2024 |
| R-4.5-win-x86_64 | OK | Nov 25 2024 |
| R-4.5-linux-x86_64 | OK | Nov 25 2024 |
| R-4.4-win-x86_64 | OK | Nov 25 2024 |
| R-4.4-mac-x86_64 | OK | Nov 25 2024 |
| R-4.4-mac-aarch64 | OK | Nov 25 2024 |
| R-4.3-win-x86_64 | OK | Nov 25 2024 |
| R-4.3-mac-x86_64 | OK | Nov 25 2024 |
| R-4.3-mac-aarch64 | OK | Nov 25 2024 |
Exports:bsseq_to_edgerbsseq_to_log_methy_ratiocluster_regionscreate_tabix_fileexonsexons_to_genesexons<-filter_methyget_cgi_grcm39get_cgi_hg19get_cgi_hg38get_cgi_mm10get_example_exons_mus_musculusget_exons_grcm39get_exons_hg19get_exons_hg38get_exons_homo_sapiensget_exons_mm10get_exons_mus_musculusload_example_modbamresultload_example_nanomethresultmethymethy_col_namesmethy_to_bsseqmethy_to_edgermethy<-mod_codemod_code<-modbam_to_tabixModBamFilesModBamResultNanoMethResultplot_agg_genesplot_agg_regionsplot_geneplot_gene_heatmapplot_grangeplot_grange_heatmapplot_mdsplot_pcaplot_regionplot_region_heatmapplot_violinquery_exons_gene_idquery_exons_regionquery_exons_symbolquery_methyregion_methy_statssamplessamples<-showsigmoid
Dependencies:abindAnnotationDbiaskpassassertthatassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocIOBiocParallelBiocSingularBiostringsbitbit64bitopsblobBSgenomebsseqcachemCairoclassclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbscanDelayedArrayDelayedMatrixStatsdplyre1071fansifarverfastmapforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggbeeswarmggplot2ggrastrgluegtablegtoolsHDF5ArrayhmshttrIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpermutepillarpkgconfigplogrpngprettyunitsprogressproxypurrrR.methodsS3R.ooR.utilsR6raggRColorBrewerRcppRCurlreadrrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitersvdrtracklayerS4ArraysS4VectorsScaledMatrixscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviporviridisLitevroomwithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert BSseq object to edgeR methylation matrix | bsseq_to_edger |
| Convert BSseq object to log-methylation-ratio matrix | bsseq_to_log_methy_ratio |
| Cluster reads based on methylation | cluster_reads |
| Cluster regions by K-means | cluster_regions |
| Create a tabix file using methylation calls | create_tabix_file |
| Convert exon annotation to genes | exons_to_genes |
| Create filtered methylation file | filter_methy |
| Get exon annotations | get_cgi_grcm39 get_cgi_hg19 get_cgi_hg38 get_cgi_mm10 get_exons get_exons_grcm39 get_exons_hg19 get_exons_hg38 get_exons_mm10 |
| Get example exon annotations for mus musculus (mm10) | get_example_exons_mus_musculus |
| Get exon annotations for Homo sapiens (hg19) | get_exons_homo_sapiens |
| Get exon annotations for Mus musculus (mm10) | get_exons_mus_musculus |
| Load an example ModBamResult object | load_example_modbamresult |
| Load an example NanoMethResult object | load_example_nanomethresult |
| Column names for methylation data | methy_col_names |
| Create BSSeq object from methylation tabix file | methy_to_bsseq |
| Convert NanoMethResult object to edgeR methylation matrix | methy_to_edger |
| Convert BAM with modifications to tabix format | modbam_to_tabix |
| Constructor for a ModBamFiles object | ModBamFiles show,ModBamFiles-method |
| ModBamFiles class | ModBamFiles-class |
| Modbam methylation results | exons,ModBamResult-method exons<-,ModBamResult,data.frame-method methy,ModBamResult-method methy<-,ModBamResult,ModBamFiles-method ModBamResult ModBamResult-class mod_code,ModBamResult-method mod_code<-,ModBamResult,character-method samples,ModBamResult-method samples<-,ModBamResult,data.frame-method |
| Nanopore Methylation Result | exons,NanoMethResult-method exons<-,NanoMethResult,data.frame-method methy,NanoMethResult-method methy<-,NanoMethResult,ANY-method NanoMethResult NanoMethResult-class samples,NanoMethResult-method samples<-,NanoMethResult,data.frame-method |
| Plot gene aggregate plot | plot_agg_genes |
| Plot aggregate regions | plot_agg_regions |
| Plot gene methylation | plot_gene plot_gene,ModBamResult,character-method plot_gene,NanoMethResult,character-method |
| Plot gene methylation heatmap | plot_gene_heatmap plot_gene_heatmap,ModBamResult,character-method plot_gene_heatmap,NanoMethResult,character-method |
| Plot GRanges | plot_grange |
| Plot GRanges heatmap | plot_grange_heatmap |
| Plot MDS | plot_mds |
| Plot PCA | plot_pca |
| Plot region methylation | plot_region plot_region,ModBamResult,character,numeric,numeric-method plot_region,ModBamResult,factor,numeric,numeric-method plot_region,NanoMethResult,character,numeric,numeric-method plot_region,NanoMethResult,factor,numeric,numeric-method |
| Plot region methylation heatmap | plot_region_heatmap plot_region_heatmap,ModBamResult,character,numeric,numeric-method plot_region_heatmap,ModBamResult,factor,numeric,numeric-method plot_region_heatmap,NanoMethResult,character,numeric,numeric-method plot_region_heatmap,NanoMethResult,factor,numeric,numeric-method |
| Plot violin for regions | plot_violin |
| Query exons | query_exons query_exons_gene_id query_exons_region query_exons_symbol |
| Query methylation data | query_methy |
| Calculate region methylation statistics | region_methy_stats |
