# Set of 3D genomic interaction analysis tools

## Documentation for package ‘HicAggR’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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
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.
preparePlotgardener | preparePlotgardener
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.