Set of 3D genomic interaction analysis tools

---

Documentation for package ‘HicAggR’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Aggregation	Aggregation of matrices list.
BalanceHiC	Compute HiC matrix-balancing.
Beaf32_Peaks.gnr	D.melanogaster Beaf-32 ChIP-seq.
BinGRanges	Bin a GRanges.
CompareToBackground	CompareToBackground
CutHiC	Cut HiC map in chunks.
ExtractSubmatrix	Submatrix extraction.
FilterInteractions	Submatrix or Interactions filtering.
GenomicSystem	Base pairs convertion.
GetInfo	get some basic information about your hic file
GetQuantif	Compute quantification on extracted submatrices.
ggAPA	Aggregation plot
HiC_Ctrl.cmx_lst	In situ Hi-C control.
HiC_HS.cmx_lst	In situ Hi-C heat treated.
Hue	Hue palette.
ICEnorm	Compute Iterative Correction.
ImportHiC	Import Hic data
ImportLoops	ImportLoops: import called loops in .bedpe format to use in HicAggR
IndexFeatures	Indexes GRanges on genome.
JoinHiC	Merge HiC chunk.
MergeGRanges	Merge GRanges.
OrientateMatrix	Matrix orientation
OverExpectedHiC	Genomic distance bias correction.
PlotAPA	Draw aggregation plot.
plotMultiAPA	Draw aggregation plots for interactions with different distances.
PrepareMtxList	Prepare matrices list for further analysis.
SearchPairs	Creates pairs from genomic index.
SeqEnds	Get all sequences lengths.
StrToGRanges	Convert String to GRanges.
SwitchMatrix	Change values of HiC map.
TADs_Domains.gnr	D.melanogaster TADs.
TSS_Peaks.gnr	D.melanogaster Transcription starting sites.
VCnorm	Compute Vanilla Count Correction.
viridis	viridis palette.
YlGnBu	YlGnBu palette.
YlOrRd	YlOrRd palette.