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

add_cluster_annotationadd_cluster_annotation
append_ynormappend_ynorm
applyMovingAverageapplyMovingAverage
applySplineapplies a spline smoothing to a tidy data.table containing x...
assemble_heatmap_cluster_barsassemble_heatmap_cluster_bars
Bcell_peaks4 random peaks for paired-end data
calc_norm_factorscalc_norm_factors
centerAtMaxcenters profile of x and y. default is to center by region...
centerFixedSizeGRangesTransforms set of GRanges to all have the same size.
centerGRangesAtMaxCenters query GRanges at maximum signal in prof_dt.
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.)...
collapse_grcollapse_gr
convert_collapsed_coordconvert_collapsed_coord
copy_clust_infocopy_clust_info
crossCorrByRleCalculate cross correlation by using shiftApply on read...
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....
dot-rm_dupesPERemove duplicate paired-end reads based on start and end...
easyLoad_bedeasyLoad_bed takes a character vector of file paths to bed...
easyLoad_broadPeakeasyLoad_broadPeak takes a character vector of file paths to...
easyLoad_FUNeasyLoad_FUN takes a character vector of file paths run an...
easyLoad_IDRmergedeasyLoad_IDRmerged loads "overlapped-peaks.txt" from IDR.
easyLoad_narrowPeakeasyLoad_narrowPeak takes a character vector of file paths to...
easyLoad_seacreasyLoad_seacr takes a character vector of file paths to...
expandCigarExpand cigar codes to GRanges
fetchBamfetch a bam file pileup with the ability to consider read...
findMaxPosfindMaxPos
fragLen_calcStrandedcalculate fragLen from a bam file for specified regions
fragLen_fromMacs2Xlsparse fragLen from MACS2 output
get_mapped_readsget_mapped_reads
getReadLengthdetermine the most common read length for input bam_file....
ggellipsereturns a ggplot with ellipses drawn using specified...
harmonize_seqlengthsharmonize_seqlengths
make_clustering_matrixmake_clustering_matrix
merge_clustersmerge_clusters
prepare_fetch_GRangesprepares GRanges for windowed fetching.
prepare_fetch_GRanges_namesCreates a named version of input GRanges using the same...
prepare_fetch_GRanges_widthprepares GRanges for windowed fetching.
quantileGRangesWidthQuantile width determination strategy
reorder_clusters_hclustreorder_clusters_hclust
reorder_clusters_manualreorder_clusters_manual
reorder_clusters_stepdownreorder_clusters_stepdown
reverse_clustersreverse_clusters
safeBrewAllows RColorBrew to handle n values less than 3 and greater...
seqsetvis-packageeasy awesome peak set vis TESTING seqsetvis allows you to...
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...
split_clustersplit_cluster
ssvConsensusIntervalSetsIntersect a list of GRanges to create a single GRanges object...
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
ssvFeatureUpsetssvFeatureUpset
ssvFeatureVennggplot implementation of vennDiagram from limma package....
ssvFetchBamIterates a character vector (ideally named) and calls...
ssvFetchBamPEssvFetchBam for paired-end ChIP-seq files. Only concordant...
ssvFetchBamPE.singlefetch a windowed version of a paired-end bam file, returns...
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.
ssvFetchGRangesFetch coverage values for a list of GRanges.
ssvFetchSignalsignal loading framework
ssvMakeMembTable-methodsgeneric for methods to convert various objects to a logical...
ssv_mclapplyssv_mclapply
ssvOverlapIntervalSetsIntersect a list of GRanges to create a single GRanges object...
ssvSignalBandedQuantilesplot profiles from bigwigs
ssvSignalClusteringClustering as for a heatmap. This is used internally by...
ssvSignalHeatmapheatmap style representation of membership table. instead of...
ssvSignalHeatmap.ClusterBarsheatmap 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...
test_peaks4 random peaks for single-end data and 4 control regions 30kb...
viewGRangesWinSample_dtget a windowed sampling of score_gr
viewGRangesWinSummary_dtSummarizes signal in bins. The same number of bins per...
within_clust_sortwithin_clust_sort
jrboyd/seqsetvis documentation built on March 17, 2024, 3:14 p.m.