Man pages for jrboyd/seqsetvis
Set Based Visualizations for Next-Gen Sequencing Data
| add_cluster_annotation | add_cluster_annotation |
| append_ynorm | append_ynorm |
| applyMovingAverage | applyMovingAverage |
| applySpline | applies a spline smoothing to a tidy data.table containing x... |
| assemble_heatmap_cluster_bars | assemble_heatmap_cluster_bars |
| Bcell_peaks | 4 random peaks for paired-end data |
| calc_norm_factors | calc_norm_factors |
| centerAtMax | centers profile of x and y. default is to center by region... |
| centerFixedSizeGRanges | Transforms set of GRanges to all have the same size. |
| centerGRangesAtMax | Centers query GRanges at maximum signal in prof_dt. |
| chromHMM_demo_bw_states_gr | MCF10A CTCF profiles at 20 windows per chromHMM state, hg38. |
| chromHMM_demo_chain_url | URL to download hg19ToHg38 liftover chain from UCSC |
| chromHMM_demo_data | chromHMM state segmentation in the MCF7 cell line |
| chromHMM_demo_overlaps_gr | overlap of MCF10A CTCF with MCF7 chromHMM states, hg38. |
| chromHMM_demo_segmentation_url | URL to download hg19 MCF7 chromHMM segmentation |
| chromHMM_demo_state_colors | original state name to color mappings stored in segmentation... |
| chromHMM_demo_state_total_widths | state name to total width mappings, hg38 |
| clusteringKmeans | perform kmeans clustering on matrix rows and return reordered... |
| clusteringKmeansNestedHclust | perform kmeans clustering on matrix rows and return reordered... |
| col2hex | converts a valid r color name ("black", "red", "white", etc.)... |
| collapse_gr | collapse_gr |
| convert_collapsed_coord | convert_collapsed_coord |
| copy_clust_info | copy_clust_info |
| crossCorrByRle | Calculate cross correlation by using shiftApply on read... |
| CTCF_in_10a_bigWig_urls | FTP URL path for vignette data. |
| CTCF_in_10a_data | CTCF ChIP-seq in breast cancer cell lines |
| CTCF_in_10a_narrowPeak_grs | list of GRanges that results in 100 random subset when... |
| CTCF_in_10a_narrowPeak_urls | FTP URL path for vignette data. from |
| CTCF_in_10a_overlaps_gr | 100 randomly selected regions from overlapping CTCF peaks in... |
| CTCF_in_10a_profiles_dt | Profiles for 100 randomly selected regions from overlapping... |
| CTCF_in_10a_profiles_gr | Profiles for 100 randomly selected regions from overlapping... |
| dot-expand_cigar_dt | Expand intermediate bam fetch by cigar codes |
| dot-expand_cigar_dt_recursive | Expand intermediate bam fetch by cigar codes |
| dot-rm_dupes | Remove duplicate reads based on stranded start position.... |
| dot-rm_dupesPE | Remove duplicate paired-end reads based on start and end... |
| easyLoad_bed | easyLoad_bed takes a character vector of file paths to bed... |
| easyLoad_broadPeak | easyLoad_broadPeak takes a character vector of file paths to... |
| easyLoad_FUN | easyLoad_FUN takes a character vector of file paths run an... |
| easyLoad_IDRmerged | easyLoad_IDRmerged loads "overlapped-peaks.txt" from IDR. |
| easyLoad_narrowPeak | easyLoad_narrowPeak takes a character vector of file paths to... |
| easyLoad_seacr | easyLoad_seacr takes a character vector of file paths to... |
| expandCigar | Expand cigar codes to GRanges |
| fetchBam | fetch a bam file pileup with the ability to consider read... |
| findMaxPos | findMaxPos |
| fragLen_calcStranded | calculate fragLen from a bam file for specified regions |
| fragLen_fromMacs2Xls | parse fragLen from MACS2 output |
| get_mapped_reads | get_mapped_reads |
| getReadLength | determine the most common read length for input bam_file.... |
| ggellipse | ggellipse |
| harmonize_seqlengths | harmonize_seqlengths |
| make_clustering_matrix | make_clustering_matrix |
| merge_clusters | merge_clusters |
| prepare_fetch_GRanges | prepares GRanges for windowed fetching. |
| prepare_fetch_GRanges_names | Creates a named version of input GRanges using the same... |
| prepare_fetch_GRanges_width | prepares GRanges for windowed fetching. |
| quantileGRangesWidth | Quantile width determination strategy |
| reorder_clusters_hclust | reorder_clusters_hclust |
| reorder_clusters_manual | reorder_clusters_manual |
| reorder_clusters_stepdown | reorder_clusters_stepdown |
| reverse_clusters | reverse_clusters |
| safeBrew | safeBrew |
| seqsetvis-package | easy awesome peak set vis TESTING seqsetvis allows you to... |
| set_list2memb | convert a list of sets, each list item should be a character... |
| shift_anchor | orients the relative position of x's zero value and extends... |
| split_cluster | split_cluster |
| ssvAnnotateSubjectGRanges | ssvAnnotateSubjectGRanges |
| ssvConsensusIntervalSets | Intersect a list of GRanges to create a single GRanges object... |
| ssvFactorizeMembTable | Convert any object accepted by ssvMakeMembTable to a factor... |
| ssvFeatureBars | bar plots of set sizes |
| ssvFeatureBinaryHeatmap | ssvFeatureBinaryHeatmap |
| ssvFeatureEuler | Try to load a bed-like file and convert it to a GRanges... |
| ssvFeaturePie | ssvFeaturePie |
| ssvFeatureUpset | ssvFeatureUpset |
| ssvFeatureVenn | ssvFeatureVenn |
| ssvFetchBam | Iterates a character vector (ideally named) and calls... |
| ssvFetchBamPE | ssvFetchBam for paired-end ChIP-seq files. Only concordant... |
| ssvFetchBamPE.RNA | ssvFetchBamPE.RNA |
| ssvFetchBamPE.single | fetch a windowed version of a paired-end bam file, returns... |
| ssvFetchBam.single | fetch a windowed version of a bam file, returns GRanges |
| ssvFetchBigwig | Iterates a character vector (ideally named) and calls... |
| ssvFetchBigwig.single | Fetch values from a bigwig appropriate for heatmaps etc. |
| ssvFetchGRanges | Fetch coverage values for a list of GRanges. |
| ssvFetchSignal | signal loading framework |
| ssvMakeMembTable-methods | generic for methods to convert various objects to a logical... |
| ssv_mclapply | ssv_mclapply |
| ssvOverlapIntervalSets | Intersect a list of GRanges to create a single GRanges object... |
| ssvSignalBandedQuantiles | plot profiles from bigwigs |
| ssvSignalClustering | Clustering as for a heatmap. This is used internally by... |
| ssvSignalHeatmap | heatmap style representation of membership table. instead of... |
| ssvSignalHeatmap.ClusterBars | heatmap style representation of membership table. instead of... |
| ssvSignalLineplot | construct line type plots where each region in each sample is... |
| ssvSignalLineplotAgg | aggregate line signals in a single line plot |
| ssvSignalScatterplot | maps signal from 2 sample profiles to the x and y axis. axes... |
| test_peaks | 4 random peaks for single-end data and 4 control regions 30kb... |
| viewGRangesWinSample_dt | get a windowed sampling of score_gr |
| viewGRangesWinSummary_dt | Summarizes signal in bins. The same number of bins per... |
| within_clust_sort | within_clust_sort |
