Shians/NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing

Package index
Search the Shians/NanoMethViz package
Vignettes
Functions
228
Source code
75
Man pages
49
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Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing
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API

API for Shians/NanoMethViz
Visualise methylation data from Oxford Nanopore sequencing

Global functions
.onLoad Source code
ModBamFiles Man page Source code
ModBamFiles-class Man page
ModBamResult Man page Source code
ModBamResult-class Man page
NanoMethResult Man page Source code
NanoMethResult-class Man page
NanoMethViz Man page
NanoMethViz-package Man page
add_read_anno Source code
assert_has_columns Source code
assert_has_index Source code
assert_readable Source code
binarise_statistics Source code
bsseq_to_edger Man page Source code
bsseq_to_edger.get_edger_col_names Source code
bsseq_to_edger.get_edger_row_names Source code
bsseq_to_edger.get_me_mat Source code
bsseq_to_edger.get_un_mat Source code
bsseq_to_log_methy_ratio Man page Source code
can_open_tabix Source code
cigar_tokeniser_cpp Source code
cluster_reads Man page Source code
cluster_regions Man page Source code
confidence_weighted_mean Source code
convert_methy_format Man page Source code
convert_methy_to_dss Source code
convert_methy_to_dss_cpp Source code
count_cg_cpp Source code
create_bsseq_from_files Source code
create_tabix_file Man page Source code
df_to_matrix Source code
empty_methy_query_output Source code
exons Man page
exons,ModBamResult-method Man page
exons,NanoMethResult-method Man page
exons<- Man page
exons<-,ModBamResult,data.frame-method Man page
exons<-,NanoMethResult,data.frame-method Man page
exons_to_genes Man page Source code
expand_motifs Source code
expect_ncol Source code
expect_nrow Source code
extract_file_names Source code
f5c_col_types Source code
filter_methy Man page Source code
gene_pos_range Source code
get_bam_total_reads Source code
get_cgi Man page Source code
get_cgi_GRCm39 Man page Source code
get_cgi_hg19 Man page Source code
get_cgi_hg38 Man page Source code
get_cgi_mm10 Man page Source code
get_char_pos_cpp Source code
get_coord_map_cpp Source code
get_example_exons_mus_musculus Man page Source code
get_exons Man page Source code
get_exons_grcm39 Man page Source code
get_exons_hg19 Man page Source code
get_exons_hg38 Man page Source code
get_exons_homo_sapiens Man page Source code
get_exons_mm10 Man page Source code
get_exons_mus_musculus Man page Source code
get_read_entropy Source code
get_read_stats Source code
get_region_methy_stats Source code
get_tabix_sequences Source code
guess_input_type Source code
guess_methy_source Source code
is_coordinate Source code
join_samples_anno Source code
load_example_modbamresult Man page Source code
load_example_nanomethresult Man page Source code
logit Source code
lollipop Source code
make_granges Source code
map_rows Source code
mat_col_map Source code
mat_row_map Source code
megalodon_col_types Source code
megalodon_col_types_old Source code
merge_methy_files Source code
methy Man page
methy,ModBamResult-method Man page
methy,NanoMethResult-method Man page
methy<- Man page
methy<-,ModBamResult,ModBamFiles-method Man page
methy<-,NanoMethResult,ANY-method Man page
methy_col_names Man page Source code
methy_col_types Source code
methy_to_bsseq Man page Source code
methy_to_edger Man page Source code
missingness Source code
mod_code Man page
mod_code,ModBamResult-method Man page
mod_code<- Man page
mod_code<-,ModBamResult,character-method Man page
mod_tokeniser_cpp Source code
modbam_to_tabix Man page Source code
nanopolish_col_types Source code
neg_strand_offset Source code
package_check Source code
parse_bam_cpp Source code
parse_bam_list Source code
parse_bam_list_cpp Source code
parse_modbam Source code
plot_agg_genes Man page Source code
plot_agg_regions Man page Source code
plot_agg_regions.avg_over_bins Source code
plot_agg_regions.get_methy_data Source code
plot_agg_regions.process_methy_data Source code
plot_agg_regions.unnest_with_anno Source code
plot_agg_tes Source code
plot_agg_tss Source code
plot_clustered_reads Source code
plot_gene Man page
plot_gene,ModBamResult,character-method Man page
plot_gene,NanoMethResult,character-method Man page
plot_gene_annotation Source code
plot_gene_heatmap Man page
plot_gene_heatmap,ModBamResult,character-method Man page
plot_gene_heatmap,NanoMethResult,character-method Man page
plot_gene_heatmap_impl Source code
plot_gene_impl Source code
plot_grange Man page Source code
plot_grange_heatmap Man page Source code
plot_mds Man page Source code
plot_methy_data_heatmap Source code
plot_methylation_data Source code
plot_pca Man page Source code
plot_region Man page
plot_region,ModBamResult,character,numeric,numeric-method Man page
plot_region,ModBamResult,factor,numeric,numeric-method Man page
plot_region,NanoMethResult,character,numeric,numeric-method Man page
plot_region,NanoMethResult,factor,numeric,numeric-method Man page
plot_region_heatmap Man page
plot_region_heatmap,ModBamResult,character,numeric,numeric-metho Man page
plot_region_heatmap,ModBamResult,factor,numeric,numeric-method Man page
plot_region_heatmap,NanoMethResult,character,numeric,numeric-met Man page
plot_region_heatmap,NanoMethResult,factor,numeric,numeric-method Man page
plot_region_heatmap_impl Source code
plot_region_impl Source code
plot_violin Man page Source code
query_exons Man page
query_exons_gene_id Man page Source code
query_exons_region Man page Source code
query_exons_symbol Man page Source code
query_methy Man page Source code
query_methy_df Source code
query_methy_gene Source code
query_methy_gr Source code
query_methy_modbam Source code
query_methy_tabix Source code
raw_methy_to_tabix Man page Source code
read_bam Source code
read_methy_lines Source code
reexports Man page
reformat_f5c Source code
reformat_megalodon Source code
reformat_nanopolish Source code
region_methy_stats Man page Source code
rolling_average Source code
run_modbam_to_tsv_converter Source code
same_length Source code
samples Man page
samples,ModBamResult-method Man page
samples,NanoMethResult-method Man page
samples<- Man page
samples<-,ModBamResult,data.frame-method Man page
samples<-,NanoMethResult,data.frame-method Man page
scale_cb_d Source code
show,ModBamFiles-method Man page
sigmoid Man page
sort_methy_file Man page Source code
stack_plots Source code
stacked_interval_inds Source code
stacked_intervals Source code
stat_lm Source code
stat_lowess Source code
tabix_compress Source code
tabix_index Source code
timed_log Source code
vec_zip Source code
write_bam_to_tsv_with_prog Source code
Shians/NanoMethViz documentation built on June 8, 2024, 10:48 p.m.

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