Package: seqsetvis 1.33.3

Joseph R Boyd

seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Authors:Joseph R Boyd [aut, cre]

seqsetvis_1.33.3.tar.gz
seqsetvis_1.33.3.zip(r-4.7-any)seqsetvis_1.33.3.zip(r-4.6-any)seqsetvis_1.33.3.zip(r-4.5-any)
seqsetvis_1.33.3.tgz(r-4.6-any)seqsetvis_1.33.3.tgz(r-4.5-any)
seqsetvis_1.33.3.tar.gz(r-4.7-any)seqsetvis_1.33.3.tar.gz(r-4.6-any)
seqsetvis_1.33.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seqsetvis/json (API)

# Install 'seqsetvis' in R:

install.packages('seqsetvis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Bcell_peaks - 4 random peaks for paired-end data
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_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
CTCF_in_10a_bigWig_urls - FTP URL path for vignette data.
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
test_peaks - 4 random peaks for single-end data and 4 control regions 30kb downstream from each peak.

On BioConductor:seqsetvis-1.33.0(bioc 3.24)seqsetvis-1.32.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software chipseq multiplecomparison sequencing visualization

5.70 score 84 scripts 641 downloads 2 mentions 69 exports 74 dependencies

Last updated from:7b4db88343. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	167
linux-devel	OK	581
source / vignettes	OK	325
linux-release	OK	544
macos-release	OK	412
macos-oldrel	OK	375
windows-devel	OK	451
windows-release	OK	479
windows-oldrel	OK	414
wasm-release	OK	173

Exports:add_cluster_annotation append_ynorm applyMovingAverage applySpline assemble_heatmap_cluster_bars calc_norm_factors centerAtMax centerFixedSizeGRanges centerGRangesAtMax clusteringKmeans clusteringKmeansNestedHclust col2hex collapse_gr convert_collapsed_coord copy_clust_info crossCorrByRle easyLoad_bed easyLoad_broadPeak easyLoad_FUN easyLoad_IDRmerged easyLoad_narrowPeak easyLoad_seacr expandCigar findMaxPos fragLen_calcStranded fragLen_fromMacs2Xls get_mapped_reads getReadLength ggellipse harmonize_seqlengths make_clustering_matrix merge_clusters prepare_fetch_GRanges prepare_fetch_GRanges_names prepare_fetch_GRanges_width quantileGRangesWidth reorder_clusters_hclust reorder_clusters_manual reorder_clusters_stepdown reverse_clusters safeBrew split_cluster ssvAnnotateSubjectGRanges ssvConsensusIntervalSets ssvFactorizeMembTable ssvFeatureBars ssvFeatureBinaryHeatmap ssvFeatureEuler ssvFeaturePie ssvFeatureUpset ssvFeatureVenn ssvFetchBam ssvFetchBamPE ssvFetchBamPE.RNA ssvFetchBigwig ssvFetchGRanges ssvFetchSignal ssvMakeMembTable ssvOverlapIntervalSets ssvSignalBandedQuantiles ssvSignalClustering ssvSignalHeatmap ssvSignalHeatmap.ClusterBars ssvSignalLineplot ssvSignalLineplotAgg ssvSignalScatterplot viewGRangesWinSample_dt viewGRangesWinSummary_dt within_clust_sort

Dependencies:askpass BH BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli codetools cowplot cpp11 crayon curl data.table digest eulerr farver formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify glue gridExtra gridGraphics gtable httr IRanges isoband jsonlite labeling lambda.r lifecycle limma mime openssl pbapply pbmcapply plyr png R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Vectors S7 scales Seqinfo snow statmod sys UCSC.utils UpSetR vctrs viridisLite withr XML XVector yaml yulab.utils

The seqsetvis package

Rendered fromseqsetvis_overview.Rmdusingknitr::rmarkdown

Last update: 2024-05-15
Started: 2018-03-29

Help page	Topics
easy awesome peak set vis TESTING seqsetvis allows you to...	seqsetvis-package seqsetvis
Expand intermediate bam fetch by cigar codes	.expand_cigar_dt
Expand intermediate bam fetch by cigar codes	.expand_cigar_dt_recursive
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_dupes
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	.rm_dupesPE
add_cluster_annotation	add_cluster_annotation
append_ynorm	append_ynorm
applyMovingAverage	applyMovingAverage
applies a spline smoothing to a tidy data.table containing x and y values.	applySpline
assemble_heatmap_cluster_bars	assemble_heatmap_cluster_bars
4 random peaks for paired-end data	Bcell_peaks
calc_norm_factors	calc_norm_factors
centers profile of x and y. default is to center by region but across all samples.	centerAtMax
Transforms set of GRanges to all have the same size.	centerFixedSizeGRanges
Centers query GRanges at maximum signal in prof_dt.	centerGRangesAtMax
MCF10A CTCF profiles at 20 windows per chromHMM state, hg38.	chromHMM_demo_bw_states_gr
URL to download hg19ToHg38 liftover chain from UCSC	chromHMM_demo_chain_url
chromHMM state segmentation in the MCF7 cell line	chromHMM_demo_data
overlap of MCF10A CTCF with MCF7 chromHMM states, hg38.	chromHMM_demo_overlaps_gr
URL to download hg19 MCF7 chromHMM segmentation	chromHMM_demo_segmentation_url
original state name to color mappings stored in segmentation bed	chromHMM_demo_state_colors
state name to total width mappings, hg38	chromHMM_demo_state_total_widths
perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments. clusters are sorted using hclust on centers	clusteringKmeans
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	clusteringKmeansNestedHclust
converts a valid r color name ("black", "red", "white", etc.) to a hex value	col2hex
collapse_gr	collapse_gr
convert_collapsed_coord	convert_collapsed_coord
copy_clust_info	copy_clust_info
Calculate cross correlation by using shiftApply on read coverage Rle	crossCorrByRle
FTP URL path for vignette data.	CTCF_in_10a_bigWig_urls
CTCF ChIP-seq in breast cancer cell lines	CTCF_in_10a_data
list of GRanges that results in 100 random subset when overlapped	CTCF_in_10a_narrowPeak_grs
FTP URL path for vignette data. from	CTCF_in_10a_narrowPeak_urls
100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq	CTCF_in_10a_overlaps_gr
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_dt
Profiles for 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq Results from CTCF_in_10a_overlaps_gr	CTCF_in_10a_profiles_gr
easyLoad_bed takes a character vector of file paths to bed plus files and returning named list of GRanges.	easyLoad_bed
easyLoad_broadPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of GRanges.	easyLoad_broadPeak
easyLoad_FUN takes a character vector of file paths run an arbitrary function defined in load_FUN	easyLoad_FUN
easyLoad_IDRmerged loads "overlapped-peaks.txt" from IDR.	easyLoad_IDRmerged
easyLoad_narrowPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of GRanges.	easyLoad_narrowPeak
easyLoad_seacr takes a character vector of file paths to seacr output bed files and returns a named list of GRanges.	easyLoad_seacr
Expand cigar codes to GRanges	expandCigar
fetch a bam file pileup with the ability to consider read extension to fragment size (fragLen)	fetchBam
findMaxPos	findMaxPos
calculate fragLen from a bam file for specified regions	fragLen_calcStranded
parse fragLen from MACS2 output	fragLen_fromMacs2Xls
get_mapped_reads	get_mapped_reads
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.	getReadLength
ggellipse	ggellipse
harmonize_seqlengths	harmonize_seqlengths
make_clustering_matrix	make_clustering_matrix
merge_clusters	merge_clusters
prepares GRanges for windowed fetching.	prepare_fetch_GRanges
Creates a named version of input GRanges using the same method seqsetvis uses internally to ensure consistency.	prepare_fetch_GRanges_names
prepares GRanges for windowed fetching.	prepare_fetch_GRanges_width
Quantile width determination strategy	quantileGRangesWidth
reorder_clusters_hclust	reorder_clusters_hclust
reorder_clusters_manual	reorder_clusters_manual
reorder_clusters_stepdown	reorder_clusters_stepdown
reverse_clusters	reverse_clusters
safeBrew	safeBrew
convert a list of sets, each list item should be a character vector denoting items in sets	set_list2memb
orients the relative position of x's zero value and extends ranges to be contiguous	shift_anchor
split_cluster	split_cluster
ssv_mclapply	ssv_mclapply
ssvAnnotateSubjectGRanges	ssvAnnotateSubjectGRanges ssvAnnotateSubjectGRanges,GRanges-method ssvAnnotateSubjectGRanges,GRangesList-method ssvAnnotateSubjectGRanges,list-method
Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges.	ssvConsensusIntervalSets
Convert any object accepted by ssvMakeMembTable to a factor To avoid ambiguity,	ssvFactorizeMembTable
bar plots of set sizes	ssvFeatureBars
ssvFeatureBinaryHeatmap	ssvFeatureBinaryHeatmap
Try to load a bed-like file and convert it to a GRanges object	ssvFeatureEuler
ssvFeaturePie	ssvFeaturePie
ssvFeatureUpset	ssvFeatureUpset
ssvFeatureVenn	ssvFeatureVenn
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
fetch a windowed version of a bam file, returns GRanges	ssvFetchBam.single
ssvFetchBam for paired-end ChIP-seq files. Only concordant reads are considered, but this has been minimally tested, please verify.	ssvFetchBamPE
ssvFetchBamPE.RNA	ssvFetchBamPE.RNA
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.	ssvFetchBamPE.single
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
Fetch values from a bigwig appropriate for heatmaps etc.	ssvFetchBigwig.single
Fetch coverage values for a list of GRanges.	ssvFetchGRanges
signal loading framework	ssvFetchSignal
generic for methods to convert various objects to a logical matrix indicating membership of items (rows) in sets (columns)	ssvMakeMembTable ssvMakeMembTable,data.frame-method ssvMakeMembTable,DataFrame-method ssvMakeMembTable,GRanges-method ssvMakeMembTable,GRangesList-method ssvMakeMembTable,list-method ssvMakeMembTable,matrix-method
Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges	ssvOverlapIntervalSets
plot profiles from bigwigs	ssvSignalBandedQuantiles
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.	ssvSignalClustering
heatmap style representation of membership table. instead of clustering, each column is sorted starting from the left.	ssvSignalHeatmap
heatmap style representation of membership table. instead of clustering, each column is sorted starting from the left.	ssvSignalHeatmap.ClusterBars
construct line type plots where each region in each sample is represented	ssvSignalLineplot
aggregate line signals in a single line plot	ssvSignalLineplotAgg
maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X	ssvSignalScatterplot
4 random peaks for single-end data and 4 control regions 30kb downstream from each peak.	test_peaks
get a windowed sampling of score_gr	viewGRangesWinSample_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.	viewGRangesWinSummary_dt
within_clust_sort	within_clust_sort

Package: seqsetvis 1.33.3

seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

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