Changes in version 0.99.0                        

Initial submission to Bioconductor.

New features

loopQTL maps chromatin loop QTLs from Hi-C: which SNPs at a loop's
anchors associate with the loop's contact strength across samples. The
package tests only SNPs that fall inside a loop's anchor bins rather
than every SNP in a wide cis-window, so signal is concentrated on the
variants biologically relevant to whether that specific loop forms.

The full workflow is documented in the package vignette with below
functions included:

  - loopQTLsetup() -- Validate inputs and build loopQTL object.
  - loopQTLnormalize() -- Cross-normalization on Hi-C signal.
  - loopQTLchooseK() -- Auto-select the number of PCs for covariates.
  - runQTL() -- Anchor-restricted association testing.
  - loopQTLpairData() -- Sample-level view of one loop × SNP pair.
  - loopQTLannotate() -- Annotate loopQTL results with target genes and
    regulatory peaks.
  - loopQTLplotPair() -- Per-sample boxplot for a single SNP-loop pair.
  - loopQTLplotLocus() -- Locus-level track view of loops, SNPs, and
    genes.
  - loopQTLplotSnpWindow() -- Hi-C-style beta heatmap around a SNP.

Example data

A 10-sample Hi-C test dataset is bundled under inst/extdata/. So the
vignette, and the example function documentation run end-to-end without
external downloads.