Man pages for jrboyd/seqsetvis
Set Based Visualizations for Next-Gen Sequencing Data

applySplineapplies a spline smoothing to a tidy data.table containing x...
centerAtMaxcenters profile of x and y. default is to center by region...
centerFixedSizeGRangesTransforms set of GRanges to all have the same size.
chromHMM_demo_bw_states_grMCF10A CTCF profiles at 20 windows per chromHMM state, hg38.
chromHMM_demo_chain_urlURL to download hg19ToHg38 liftover chain from UCSC
chromHMM_demo_datachromHMM state segmentation in the MCF7 cell line
chromHMM_demo_overlaps_groverlap of MCF10A CTCF with MCF7 chromHMM states, hg38.
chromHMM_demo_segmentation_urlURL to download hg19 MCF7 chromHMM segmentation
chromHMM_demo_state_colorsoriginal state name to color mappings stored in segmentation...
chromHMM_demo_state_total_widthsstate name to total width mappings, hg38
clusteringKmeansperform kmeans clustering on matrix rows and return reordered...
clusteringKmeansNestedHclustperform kmeans clustering on matrix rows and return reordered...
col2hexconverts a valid r color name ("black", "red", "white", etc.)...
CTCF_in_10a_bigWig_urlsFTP URL path for vignette data.
CTCF_in_10a_dataCTCF ChIP-seq in breast cancer cell lines
CTCF_in_10a_narrowPeak_grslist of GRanges that results in 100 random subset when...
CTCF_in_10a_narrowPeak_urlsFTP URL path for vignette data. from
CTCF_in_10a_overlaps_gr100 randomly selected regions from overlapping CTCF peaks in...
CTCF_in_10a_profiles_dtProfiles for 100 randomly selected regions from overlapping...
CTCF_in_10a_profiles_grProfiles for 100 randomly selected regions from overlapping...
dot-expand_cigar_dtExpand intermediate bam fetch by cigar codes
dot-expand_cigar_dt_recursiveExpand intermediate bam fetch by cigar codes
dot-rm_dupesRemove duplicate reads based on stranded start position....
easyLoad_bedeasyLoad_bed takes a character vector of file paths to bed...
easyLoad_broadPeakeasyLoad_broadPeak takes a character vector of file paths to...
easyLoad_narrowPeakeasyLoad_narrowPeak takes a character vector of file paths to...
fetchBamfetch a bam file pileup with the ability to consider read...
fixGRangesWidthDerive a new GRanges of consistent width based on quantile.
fragLen_calcStrandedcalculate fragLen from a bam file for specified regions
fragLen_fromMacs2Xlsparse fragLen from MACS2 output
ggellipsereturns a ggplot with ellipses drawn using specified...
prepare_fetch_GRangesprepares GRanges for windowed fetching.
quantileGRangesWidthQuantile width determination strategy
safeBrewallows RColorBrew to handle n values less than 3 and greater...
seqsetvis-packageeasy awesome peak set vis TESTING seqsetvis allows you to...
setGRangesWidthReturn GRanges with single width
set_list2membconvert a list of sets, each list item should be a character...
shift_anchororients the relative position of x's zero value and extends...
ssvFactorizeMembTableConvert any object accepted by ssvMakeMembTable to a factor...
ssvFeatureBarsbar plots of set sizes
ssvFeatureBinaryHeatmapbinary heatmap indicating membership. heatmap is sorted by...
ssvFeatureEulerTry to load a bed-like file and convert it to a GRanges...
ssvFeaturePiepie plot of set sizes
ssvFeatureVennggplot implementation of vennDiagram from limma package....
ssvFetchBamIterates a character vector (ideally named) and calls...
ssvFetchBam.singlefetch a windowed version of a bam file, returns GRanges
ssvFetchBigwigIterates a character vector (ideally named) and calls...
ssvFetchBigwig.singleFetch values from a bigwig appropriate for heatmaps etc.
ssvFetchSignalGeneric signal loading function
ssvMakeMembTable-methodsgeneric for methods to convert various objects to a logical...
ssvOverlapIntervalSetsIntersect a list of GRanges to create a single GRanges object...
ssvSignalBandedQuantilesplot profiles from bigwigs
ssvSignalClusteringclustering as for a heatmap
ssvSignalHeatmapheatmap style representation of membership table. instead of...
ssvSignalLineplotconstruct line type plots where each region in each sample is...
ssvSignalLineplotAggaggregate line signals in a single line plot
ssvSignalScatterplotmaps signal from 2 sample profiles to the x and y axis. axes...
viewGRangesWinSample_dtget a windowed sampling of score_gr
viewGRangesWinSummary_dtSummarizes signal in bins. The same number of bins per...
jrboyd/seqsetvis documentation built on Aug. 31, 2018, 4:24 a.m.