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:Shian Su [cre, aut]

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'))

Bug tracker:https://github.com/shians/nanomethviz/issues

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

On BioConductor:NanoMethViz-3.1.5(bioc 3.20)NanoMethViz-3.0.2(bioc 3.19)

software longread visualization differentialmethylation dnamethylation epigenetics dataimport

7.00 score 24 stars 12 scripts 260 downloads 52 exports 140 dependencies

Last updated 23 days agofrom:1ee21fe29e. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	OK	Oct 31 2024
R-4.5-linux-x86_64	OK	Oct 30 2024
R-4.4-win-x86_64	OK	Oct 31 2024
R-4.4-mac-x86_64	OK	Oct 31 2024
R-4.4-mac-aarch64	OK	Oct 31 2024
R-4.3-win-x86_64	OK	Oct 31 2024
R-4.3-mac-x86_64	OK	Oct 31 2024
R-4.3-mac-aarch64	OK	Oct 31 2024

Exports:bsseq_to_edger bsseq_to_log_methy_ratio cluster_regions create_tabix_file exons exons_to_genes exons<-filter_methy get_cgi_grcm39 get_cgi_hg19 get_cgi_hg38 get_cgi_mm10 get_example_exons_mus_musculus get_exons_grcm39 get_exons_hg19 get_exons_hg38 get_exons_homo_sapiens get_exons_mm10 get_exons_mus_musculus load_example_modbamresult load_example_nanomethresult methy methy_col_names methy_to_bsseq methy_to_edger methy<-mod_code mod_code<-modbam_to_tabix ModBamFiles ModBamResult NanoMethResult plot_agg_genes plot_agg_regions plot_gene plot_gene_heatmap plot_grange plot_grange_heatmap plot_mds plot_pca plot_region plot_region_heatmap plot_violin query_exons_gene_id query_exons_region query_exons_symbol query_methy region_methy_stats samples samples<-show sigmoid

Dependencies:abind AnnotationDbi askpass assertthat assorthead beachmat beeswarm BH Biobase BiocGenerics BiocIO BiocParallel BiocSingular Biostrings bit bit64 bitops blob BSgenome bsseq cachem Cairo class cli clipr codetools colorspace cpp11 crayon curl data.table DBI dbscan DelayedArray DelayedMatrixStats dplyr e1071 fansi farver fastmap forcats formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggbeeswarm ggplot2 ggrastr glue gtable gtools HDF5Array hms httr IRanges irlba isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl patchwork permute pillar pkgconfig plogr png prettyunits progress proxy purrr R.methodsS3 R.oo R.utils R6 ragg RColorBrewer Rcpp RCurl readr restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools RSQLite rsvd rtracklayer S4Arrays S4Vectors ScaledMatrix scales snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vipor viridisLite vroom withr XML XVector yaml zlibbioc

User's Guide

Shian Su

Rendered fromUsersGuide.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-05-21
Started: 2023-10-17

Citation

Development and contributors

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