tanaylab/gpatterns
Single Molecule Methylation Patterns Analysis Suite

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234
Source code
22
Man pages
77
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tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite
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API

API for tanaylab/gpatterns
Single Molecule Methylation Patterns Analysis Suite

Global functions
.expand_hamming Source code
.gpatterns.arrange_biploar_model_output Source code
.gpatterns.avg_track_name Source code
.gpatterns.bam2reads Man page
.gpatterns.bam2tidy_cpgs Source code
.gpatterns.bipolar_model_file_name Source code
.gpatterns.bipolar_model_tab_name Source code
.gpatterns.center_meth_track_name Source code
.gpatterns.center_uni_track_name Source code
.gpatterns.center_unmeth_track_name Source code
.gpatterns.cov_track_name Source code
.gpatterns.downsampled_track_name Source code
.gpatterns.ds_stats Man page
.gpatterns.epipolymorphism_track_name Source code
.gpatterns.fid_track_name Source code
.gpatterns.fids_file_name Source code
.gpatterns.fids_tab_name Source code
.gpatterns.filter_coverage Source code
.gpatterns.filter_ontar_reads Man page
.gpatterns.frag_cov_track_name Source code
.gpatterns.gain_meth_track_name Source code
.gpatterns.gain_uni_track_name Source code
.gpatterns.gain_unmeth_track_name Source code
.gpatterns.get_avg_meth_not_tidy Source code
.gpatterns.get_global_meth_trend Source code
.gpatterns.get_intervals Source code
.gpatterns.loss_meth_track_name Source code
.gpatterns.loss_uni_track_name Source code
.gpatterns.loss_unmeth_track_name Source code
.gpatterns.meth_track_name Source code
.gpatterns.mix_meth_track_name Source code
.gpatterns.mix_qval_track_name Source code
.gpatterns.mix_unmeth_track_name Source code
.gpatterns.n0_track_name Source code
.gpatterns.n1_track_name Source code
.gpatterns.n_track_name Source code
.gpatterns.nc_track_name Source code
.gpatterns.ncpg_track_name Source code
.gpatterns.nx_track_name Source code
.gpatterns.pat_cov_track_name Source code
.gpatterns.pat_meth_track_name Source code
.gpatterns.pat_space_intervs_name Source code
.gpatterns.patterns_file_name Source code
.gpatterns.patterns_tab_name Source code
.gpatterns.patterns_track_names Source code
.gpatterns.reads_per_umi Man page
.gpatterns.run_bipolar_model Source code
.gpatterns.save_bipolar_stats Source code
.gpatterns.special_intervals Source code
.gpatterns.stats_file_name Source code
.gpatterns.tidy_cpgs_dir Source code
.gpatterns.tidy_cpgs_files Source code
.gpatterns.unmeth_track_name Source code
.gpwm.verify_jobs_successes Source code
.gpwm_cache_misses Source code
.gtrack.union_intervals Source code
.onLoad Source code
.random_track_name Source code
.split2char Source code
.step_invoke Source code
.unite_by_char Source code
TGL_kmeans Man page Source code
TGL_kmeans2 Man page
add_file_path Source code
apply_genome_conf Source code
blue_message Source code
build_pallette Man page
conf2index Source code
cume_dist_min Man page Source code
demultiplex_fastqs Source code
demultiplex_per_index Source code
fill_hamming Source code
gbin_intervals Man page Source code
gcluster.run2 Man page
gdply Man page Source code
get_raw_reads_files Source code
gextract.left_join Man page Source code
gintervals.center Source code
gintervals.centers Source code
gintervals.distance Source code
gintervals.expand Source code
gintervals.filter Man page Source code
gintervals.left_join Source code
gintervals.mark_overlapping Source code
gintervals.neighbors1 Man page Source code
gintervals.neighbors_y Source code
gintervals.normalize Source code
gintervals.which Source code
glply Man page Source code
gmax.coord Source code
gpatterns Man page
gpatterns.adjust_read_pos Man page
gpatterns.apply_tidy_cpgs Man page Source code
gpatterns.bam2tracks Source code
gpatterns.bissli2 Man page Source code
gpatterns.bissli2_build Man page Source code
gpatterns.border_pattern Man page Source code
gpatterns.calc_bipolarity Man page
gpatterns.calc_epipoly Man page Source code
gpatterns.capture_stats Man page Source code
gpatterns.chip2peaks Man page Source code
gpatterns.clean_pattern Man page Source code
gpatterns.cluster Source code
gpatterns.conv_stats Man page
gpatterns.count_cpgs Man page Source code
gpatterns.create_patterns_track Man page
gpatterns.cutree Source code
gpatterns.demultiplex_fastqs Source code
gpatterns.demultiplexing_stats Source code
gpatterns.downsample_patterns Man page
gpatterns.epipoly_plot Man page Source code
gpatterns.extract Man page
gpatterns.extract_all Man page
gpatterns.extract_patterns Man page
gpatterns.filter_by_dist Man page Source code
gpatterns.filter_cpgs Man page Source code
gpatterns.filter_loci Man page Source code
gpatterns.frag_stats Man page
gpatterns.get_avg_meth Man page Source code
gpatterns.get_bg_meth Man page Source code
gpatterns.get_fragment_cov Man page
gpatterns.get_meth_quantile Source code
gpatterns.get_pat_cov Man page
gpatterns.get_pipeline_stats Man page Source code
gpatterns.get_promoters Man page Source code
gpatterns.get_tcpgs_stats Man page Source code
gpatterns.get_tidy_cpgs Man page Source code
gpatterns.global_meth_trend Man page Source code
gpatterns.import_from_bam Man page Source code
gpatterns.import_from_tidy_cpgs Man page Source code
gpatterns.impute Man page Source code
gpatterns.intervals_coverage Man page Source code
gpatterns.intervs_to_pat_space Man page
gpatterns.ls Man page Source code
gpatterns.map Source code
gpatterns.merge_tidy_cpgs Man page Source code
gpatterns.merge_tracks Man page
gpatterns.pipeline Man page Source code
gpatterns.plot_cg_cor Man page
gpatterns.plot_chip_quantiles Man page Source code
gpatterns.plot_clustering Source code
gpatterns.putative_enhancers Man page Source code
gpatterns.rm Man page
gpatterns.screen_by_coverage Man page Source code
gpatterns.separate_strands Man page Source code
gpatterns.set_parallel Man page
gpatterns.smoothScatter Man page Source code
gpatterns.spatial_meth_trend Man page Source code
gpatterns.theta_distance Source code
gpatterns.tidy_cpgs_2_pat_freq Man page
gpatterns.tidy_cpgs_2_pileup Man page
gpatterns.tidy_cpgs_to_pats Man page
gpatterns.track_exists Man page
gpatterns.track_pat_space Man page
gpatterns.track_stats Man page Source code
gpatterns.tracks_to_pat_space Man page
gpwm.add_global_quantiles Source code
gpwm.clear_cache Source code
gpwm.extract Source code
gpwm.extract_all Source code
gpwm.extract_motif Source code
gpwm.get_global_quantiles Source code
gpwm.load_cache Source code
gpwm.max_val_quantile Source code
gpwm.max_val_quantile_all Source code
gpwm.motif_enrich Source code
gpwm.motif_enrich_per_cluster Source code
gpwm.save_cache Source code
gseq.extract_conv Source code
gseq.rev_comp Source code
gtrack.array.import_from_df Man page Source code
gtrack.array.import_from_tracks Source code
gtrack.import_mappedseq_bam Man page Source code
gvextract Man page Source code
invoke_step Source code
list_split_fastq_files Source code
mpms Man page Source code
p_smoothScatter Man page Source code
parse_commmands_res Source code
pheatmap1 Man page
qqv Source code
red_message Source code
rm_ambig_bcds Source code
run_demultiplexing_commands Source code
run_step Source code
sum_ignore_na Source code
yaml2cfg Source code
tanaylab/gpatterns documentation built on May 15, 2023, 6:23 p.m.

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