Man pages for tanaylab/gpatterns
Single Molecule Methylation Patterns Analysis Suite
| build_pallette | Build a gradient pallete based on colors at specific values. |
| cume_dist_min | Return an alternate empirical cumulative distribution,... |
| dot-gpatterns.bam2reads | bam 2 reads |
| dot-gpatterns.ds_stats | ds stats downsampling stats |
| dot-gpatterns.filter_ontar_reads | filter on target reads Filters on target reads |
| dot-gpatterns.reads_per_umi | reads per umi |
| gbin_intervals | split genomic intervals to bins |
| gcluster.run2 | Runs R commands on a cluster that supports SGE |
| gextract.left_join | Returns the result of track expressions evaluation for each... |
| gintervals.filter | Filter intervals set by distance to another. A wrapper around... |
| gintervals.neighbors1 | Finds neighbors between two sets of intervals (and does not... |
| glply | Apply a function on track expression in intervals |
| gpatterns | gpatterns. |
| gpatterns.adjust_read_pos | Change tidy_cpgs coordinates to fragments coordinates |
| gpatterns.apply_tidy_cpgs | Apply a function on tidy cpgs (internally separated by... |
| gpatterns.bissli2 | Align bisulfite converted reads to a reference genome using... |
| gpatterns.bissli2_build | Create an bowtie2 index for a bisulfite converted genome |
| gpatterns.border_pattern | Returns TRUE if pattern is a 'border' pattern |
| gpatterns.calc_bipolarity | Run bipolar model |
| gpatterns.calc_epipoly | Calculate epipolymorphism of samples |
| gpatterns.capture_stats | Capture stats |
| gpatterns.chip2peaks | Calculate peaks of chip-seq tracks |
| gpatterns.clean_pattern | Returns TRUE if pattern is fully methylated / unmethylated... |
| gpatterns.conv_stats | converstion stats |
| gpatterns.count_cpgs | count CpGs in intervals |
| gpatterns.create_patterns_track | Creates patterns attributes of track |
| gpatterns.downsample_patterns | Downsample patterns table |
| gpatterns.epipoly_plot | Plots epipolymorphism |
| gpatterns.extract | Extract pattern data |
| gpatterns.extract_all | Extract pattern data from tracks without specifying... |
| gpatterns.extract_patterns | Extract patterns of a track |
| gpatterns.filter_by_dist | Filter intervals set by distance from another intervals set |
| gpatterns.filter_cpgs | Filter intervals by number of CpGs |
| gpatterns.filter_loci | Filter loci with low variance across samples |
| gpatterns.frag_stats | transforms patterns to summary statistics: n,n0,n1,nx,nc,meth... |
| gpatterns.get_avg_meth | Extract average methylation |
| gpatterns.get_bg_meth | Get background trend expected methylation signal |
| gpatterns.get_fragment_cov | Get fragment coverage |
| gpatterns.get_pat_cov | Calculate pattern coverage for each CpG |
| gpatterns.get_pipeline_stats | Calculate QC statistics for track |
| gpatterns.get_promoters | Define promoter regions |
| gpatterns.get_tcpgs_stats | Get QC statistics from tcpgs dir |
| gpatterns.get_tidy_cpgs | Get tidy cpgs from a track |
| gpatterns.global_meth_trend | Plot global methylation stratified on other tracks |
| gpatterns.import_from_bam | Create a track from bam files. |
| gpatterns.import_from_tidy_cpgs | Create a track from tidy_cpgs files |
| gpatterns.impute | Impute missing methylation calls |
| gpatterns.intervals_coverage | Get coverage of intervals in multiple tracks |
| gpatterns.intervs_to_pat_space | Generate pattern space for specific genomic loci |
| gpatterns.ls | Returns a list of track names |
| gpatterns.merge_tidy_cpgs | merge tidy cpgs directories |
| gpatterns.merge_tracks | Merge tracks |
| gpatterns.pipeline | Run pipeline |
| gpatterns.plot_cg_cor | Plot CpG correlation (pearson) as a function of distance... |
| gpatterns.plot_chip_quantiles | Plot chip-seq singal with quantile lines |
| gpatterns.putative_enhancers | Define putative enhancer regions from chip-seq tracks |
| gpatterns.rm | Remove gpatterns track |
| gpatterns.screen_by_coverage | screen intervals by coverage in multiple tracks |
| gpatterns.separate_strands | Separate a track by strands (for QC purposes) |
| gpatterns.set_parallel | Set parallel threads |
| gpatterns.smoothScatter | Plots smoothScatter of average methylation of two tracks |
| gpatterns.spatial_meth_trend | Plot spatial trend of methylation around intervals |
| gpatterns.tidy_cpgs_2_pat_freq | Generate CpG pattern frequency from tidy_cpgs |
| gpatterns.tidy_cpgs_2_pileup | Generate pileup form tidy_cpgs |
| gpatterns.tidy_cpgs_to_pats | Extracts patterns given pattern space |
| gpatterns.track_exists | check if tidy_cpgs exist for track |
| gpatterns.track_pat_space | Get pattern space of a track |
| gpatterns.track_stats | Get QC statistics for track |
| gpatterns.tracks_to_pat_space | Generate pattern space |
| gtrack.array.import_from_df | Import array from data frame |
| gtrack.import_mappedseq_bam | Wrapper around gtrack.import_mappedseq for (multiple) bam... |
| gvextract | Creates a virtual track and runs gextract |
| mpms | Run mpms |
| pheatmap1 | wrapper around pheatmap |
| p_smoothScatter | Smoothscatter that works with the pipe operator |
| TGL_kmeans | Effiecient implementation of kmeans++ algorithm |
| TGL_kmeans2 | Alternative interface for TGL_kmeans Returned value is more... |
