.expand_cigar_dt        Expand intermediate bam fetch by cigar codes
.expand_cigar_dt_recursive
                        Expand intermediate bam fetch by cigar codes
.rm_dupes               Remove duplicate reads based on stranded start
                        position.  This is an over-simplification.  For
                        better duplicate handling, duplicates must be
                        marked in bam and flag passed to fetchBam() ...
                        for ScanBamParam
.rm_dupesPE             Remove duplicate paired-end reads based on
                        start and end position. This is an
                        over-simplification.  For better duplicate
                        handling, duplicates must be marked in bam and
                        flag passed to fetchBamPE() ... for
                        ScanBamParam
Bcell_peaks             4 random peaks for paired-end data
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 overlapped
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 10a cell ChIP-seq
CTCF_in_10a_profiles_dt
                        Profiles for 100 randomly selected regions from
                        overlapping CTCF peaks in 10a cell ChIP-seq
                        Results from fetching bigwigs with
                        CTCF_in_10a_overlaps_gr.
CTCF_in_10a_profiles_gr
                        Profiles for 100 randomly selected regions from
                        overlapping CTCF peaks in 10a cell ChIP-seq
                        Results from CTCF_in_10a_overlaps_gr
add_cluster_annotation
                        add_cluster_annotation
append_ynorm            append_ynorm
applySpline             applies a spline smoothing to a tidy data.table
                        containing x and y values.
assemble_heatmap_cluster_bars
                        assemble_heatmap_cluster_bars
calc_norm_factors       calc_norm_factors
centerAtMax             centers profile of x and y.  default is to
                        center by region but across all samples.
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 bed
chromHMM_demo_state_total_widths
                        state name to total width mappings, hg38
clusteringKmeans        perform kmeans clustering on matrix rows and
                        return reordered matrix along with order
                        matched cluster assignments. clusters are
                        sorted using hclust on centers
clusteringKmeansNestedHclust
                        perform kmeans clustering on matrix rows and
                        return reordered matrix along with order
                        matched cluster assignments clusters are sorted
                        using hclust on centers the contents of each
                        cluster are sorted using hclust
col2hex                 converts a valid r color name ("black", "red",
                        "white", etc.) to a hex value
collapse_gr             collapse_gr
convert_collapsed_coord
                        convert_collapsed_coord
crossCorrByRle          Calculate cross correlation by using shiftApply
                        on read coverage Rle
easyLoad_bed            easyLoad_bed takes a character vector of file
                        paths to bed plus files and returning named
                        list of GRanges. Mainly a utility function for
                        loading MACS2 narrowPeak and broadPeak.
easyLoad_broadPeak      easyLoad_broadPeak takes a character vector of
                        file paths to narrowPeak files from MACS2 and
                        returns a named list of GRanges.
easyLoad_narrowPeak     easyLoad_narrowPeak takes a character vector of
                        file paths to narrowPeak files from MACS2 and
                        returns a named list of GRanges.
easyLoad_seacr          easyLoad_seacr takes a character vector of file
                        paths to seacr output bed files and returns a
                        named list of GRanges.
expandCigar             Expand cigar codes to GRanges
fetchBam                fetch a bam file pileup with the ability to
                        consider read extension to fragment size
                        (fragLen)
fragLen_calcStranded    calculate fragLen from a bam file for specified
                        regions
fragLen_fromMacs2Xls    parse fragLen from MACS2 output
getReadLength           determine the most common read length for input
                        bam_file.  uses 50 randomly selected regions
                        from query_gr.  If fewer than 20 reads are
                        present, loads all of query_gr.
ggellipse               returns a ggplot with ellipses drawn using
                        specified parameters used by ssvFeatureVenn and
                        ssvFeatureEuler
harmonize_seqlengths    harmonize_seqlengths
make_clustering_matrix
                        make_clustering_matrix
prepare_fetch_GRanges   prepares GRanges for windowed fetching.
prepare_fetch_GRanges_names
                        Creates a named version of input GRanges using
                        the same method seqsetvis uses internally to
                        ensure consistency.
prepare_fetch_GRanges_width
                        prepares GRanges for windowed fetching.
quantileGRangesWidth    Quantile width determination strategy
safeBrew                allows RColorBrew to handle n values less than
                        3 and greater than 8 without warnings and
                        return expected number of colors.
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 vector denoting items in sets
shift_anchor            orients the relative position of x's zero value
                        and extends ranges to be contiguous
ssvConsensusIntervalSets
                        Intersect a list of GRanges to create a single
                        GRanges object of merged ranges including
                        metadata describing overlaps per input GRanges.
ssvFactorizeMembTable   Convert any object accepted by ssvMakeMembTable
                        to a factor To avoid ambiguity,
ssvFeatureBars          bar plots of set sizes
ssvFeatureBinaryHeatmap
                        binary heatmap indicating membership. heatmap
                        is sorted by column left to right. change
                        column order to reveal patterns
ssvFeatureEuler         Try to load a bed-like file and convert it to a
                        GRanges object
ssvFeaturePie           pie plot of set sizes
ssvFeatureUpset         ssvFeatureUpset
ssvFeatureVenn          ggplot implementation of vennDiagram from limma
                        package.  currently limited at 3 sets.
                        ssvFeatureUpset and ssvFeatureBinaryHeatmap are
                        good options for more than 3 sets.
                        ssvFeatureEuler can work too but can take a
                        very long time to run for more than 5 or so.
ssvFetchBam             Iterates a character vector (ideally named) and
                        calls 'ssvFetchBam.single' on each.  Appends
                        grouping variable to each resulting data.table
                        and uses rbindlist to efficiently combine
                        results
ssvFetchBam.single      fetch a windowed version of a bam file, returns
                        GRanges
ssvFetchBamPE           ssvFetchBam for paired-end ChIP-seq files. Only
                        concordant reads are considered, but this has
                        been minimally tested, please verify.
ssvFetchBamPE.single    fetch a windowed version of a paired-end bam
                        file, returns GRanges In contrast to
                        ssvFetchBam, extension of reads to estimated
                        fragment size is not an issue as each read pair
                        represents a fragment of exact size.
ssvFetchBigwig          Iterates a character vector (ideally named) and
                        calls 'ssvFetchBigwig.single' on each.  Appends
                        grouping variable to each resulting data.table
                        and uses rbindlist to efficiently combine
                        results.
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        generic for methods to convert various objects
                        to a logical matrix indicating membership of
                        items (rows) in sets (columns)
ssvOverlapIntervalSets
                        Intersect a list of GRanges to create a single
                        GRanges object of merged ranges including
                        metadata describing overlaps per input GRanges
ssvSignalBandedQuantiles
                        plot profiles from bigwigs
ssvSignalClustering     Clustering as for a heatmap.  This is used
                        internally by 'ssvSignalHeatmap' but can also
                        be run before calling ssvSignalHeatmap for
                        greater control and access to clustering
                        results directly.
ssvSignalHeatmap        heatmap style representation of membership
                        table. instead of clustering, each column is
                        sorted starting from the left.
ssvSignalHeatmap.ClusterBars
                        heatmap style representation of membership
                        table. instead of clustering, each column is
                        sorted starting from the left.
ssvSignalLineplot       construct line type plots where each region in
                        each sample is represented
ssvSignalLineplotAgg    aggregate line signals in a single line plot
ssvSignalScatterplot    maps signal from 2 sample profiles to the x and
                        y axis. axes are standard or "volcano" min XY
                        vs fold-change Y/X
test_peaks              4 random peaks for single-end data and 4
                        control regions 30kb downstream from each peak.
viewGRangesWinSample_dt
                        get a windowed sampling of score_gr
viewGRangesWinSummary_dt
                        Summarizes signal in bins.  The same number of
                        bins per region in qgr is used and widths can
                        vary in qgr, in contrast to
                        'viewGRangesWinSample_dt' where width must be
                        constant across regions.
