Files in Shians/NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing
.Rbuildignore
.covrignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/check-standard.yaml
.github/workflows/test-coverage.yaml
.gitignore
.lintr
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/AllGenerics.R
R/ModBamResults.R
R/NanoMethResults.R
R/NanoMethViz-package.R
R/RcppExports.R
R/assertions.R
R/bsseq_to_edger.R
R/cluster_reads.R
R/cluster_regions.R
R/col_specs.R
R/convert_methy_format.R
R/create_tabix_file.R
R/exons_to_genes.R
R/filter_methy.R
R/get_cgi.R
R/get_exons.R
R/get_read_entropy.R
R/karyogram.R
R/lollipop.R
R/merge_methy_files.R
R/methy_to_bsseq.R
R/modbam.R
R/modbam_to_tabix.R
R/palettes.R
R/plot_agg_genes.R
R/plot_agg_regions.R
R/plot_clustered_reads.R
R/plot_gene.R
R/plot_gene_annotation.R
R/plot_gene_heatmap.R
R/plot_grange.R
R/plot_heatmap.R
R/plot_mds.R
R/plot_methylation.R
R/plot_pca.R
R/plot_region.R
R/plot_region_heatmap.R
R/plot_violin.R
R/query_exons.R
R/query_methy.R
R/reexport.R
R/region_methy_stats.R
R/stack_interval.R
R/stat_lm.R
R/stat_lowess.R
R/tabix_utils.R
R/themes.R
R/utils.R
R/utils_expect.R
R/zzz.R
README.md
codecov.yml
img/agg_genes.png
img/make_img.R
img/mds.png
img/peg3_gene.png
inst/CITATION
inst/c_elegans.gtf.gz
inst/cgi_GRCm39.rds
inst/cgi_hg19.rds
inst/cgi_hg38.rds
inst/cgi_mm10.rds
inst/create_cgi_anno.R
inst/dmr_subset.tsv.gz
inst/megalodon_calls.txt.gz
inst/methy_data_with_inf.tsv
inst/methy_subset.tsv.bgz
inst/methy_subset.tsv.bgz.tbi
inst/no_index.bam
inst/peg3.bam
inst/peg3.bam.bai
inst/peg3_lower_case.bam
inst/peg3_lower_case.bam.bai
inst/sample1_nanopolish.tsv.gz
inst/sample2_nanopolish.tsv.gz
man/ModBamFiles-class.Rd
man/ModBamFiles.Rd
man/ModBamResult-class.Rd
man/NanoMethResult-class.Rd
man/NanoMethViz-package.Rd
man/bsseq_to_edger.Rd
man/bsseq_to_log_methy_ratio.Rd
man/cluster_reads.Rd
man/cluster_regions.Rd
man/convert_methy_format.Rd
man/create_tabix_file.Rd
man/exons-set.Rd
man/exons.Rd
man/exons_to_genes.Rd
man/filter_methy.Rd
man/get_cgi.Rd
man/get_example_exons_mus_musculus.Rd
man/get_exons.Rd
man/get_exons_homo_sapiens.Rd
man/get_exons_mus_musculus.Rd
man/load_example_modbamresult.Rd
man/load_example_nanomethresult.Rd
man/methy-set.Rd
man/methy.Rd
man/methy_col_names.Rd
man/methy_to_bsseq.Rd
man/methy_to_edger.Rd
man/mod_code-set.Rd
man/mod_code.Rd
man/modbam_to_tabix.Rd
man/plot_agg_genes.Rd
man/plot_agg_regions.Rd
man/plot_gene.Rd
man/plot_gene_heatmap.Rd
man/plot_grange.Rd
man/plot_grange_heatmap.Rd
man/plot_mds.Rd
man/plot_pca.Rd
man/plot_region.Rd
man/plot_region_heatmap.Rd
man/plot_violin.Rd
man/query_exons.Rd
man/query_methy.Rd
man/raw_methy_to_tabix.Rd
man/reexports.Rd
man/region_methy_stats.Rd
man/samples-set.Rd
man/samples.Rd
man/sort_methy_file.Rd
src/Makevars
src/RcppExports.cpp
src/convert_methy_to_dss.cpp
src/convert_methy_to_dss.h
src/count_cg.cpp
src/modbam.cpp
src/utils.cpp
src/utils.h
src/zstr/strict_fstream.h
src/zstr/zstr.h
src/zstr/zstr.hpp
tests/testthat-problems.rds
tests/testthat.R
tests/testthat/test-ModBamResults.R
tests/testthat/test-NanoMethResults.R
tests/testthat/test-bsseq_to_edger.R
tests/testthat/test-cluster_reads.R
tests/testthat/test-cluster_regions.R
tests/testthat/test-filter_methy.R
tests/testthat/test-get_cgi.R
tests/testthat/test-methy_to_bsseq.R
tests/testthat/test-modbam_to_tabix.R
tests/testthat/test-plot_agg_genes.R
tests/testthat/test-plot_agg_regions.R
tests/testthat/test-plot_basic.R
tests/testthat/test-plot_gene_heatmap.R
tests/testthat/test-plot_mds.R
tests/testthat/test-plot_methylation.R
tests/testthat/test-plot_pca.R
tests/testthat/test-plot_region_heatmap.R
tests/testthat/test-query_methy.R
tests/testthat/test-region_methy_stats.R
tests/testthat/test-stack_interval.R
tests/testthat/test-tabix_utils.R
tests/testthat/test-utils.R
vignettes/UsersGuide.Rmd
