Bioconductor Hicontacts
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets...
Install
npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-hicontacts -g -a claude-code -y- Repository
- bioMate-AI/biomate-bioconductor-kb793
- Category
- Engineering
- Updated
- 5mo ago
- License
- See repository
- Context cost
- Lightabout 1,146 tokens
- Runs scripts
- No, instructions only
What it does
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
HiContacts
Workflows
Standard Workflow
library(HiCExperiment)
library(HiContacts)
library(HiContactsData)
# Import Hi-C matrix
cool_file <- HiContactsData('yeast_wt', format = 'cool')
hic <- import(cool_file, format = 'cool')
# Perform matrix arithmetic
hic_detrended <- detrend(hic)
hic_smooth <- despeckle(hic)
# Plot contact map
plotMatrix(hic_smooth, use.scores = 'balanced.despeckled')
Input: A HiCExperiment object.
Output: Detrended, smoothed, or merged contact maps and their corresponding plots.
Contact Map Analysis
library(HiCExperiment)
library(HiContacts)
library(HiContactsData)
mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
hic <- import(mcool_file, format = 'mcool', resolution = 1000)
# Calculate cis-trans ratios
ratios <- cisTransRatio(hic)
# Compute distance decay P(s) curves
ps <- distanceLaw(hic)
Input: A HiCExperiment object, optionally with an associated pairs file.
Output: A tibble of cis-trans ratios and distance decay P(s) curves.
Topological Feature Mapping
library(HiCExperiment)
library(HiContacts)
library(HiContactsData)
mcool_file <- HiContactsData('yeast_wt', format = 'mcool')
hic <- import(mcool_file, format = 'mcool', resolution = 16000)
# Map chromosome compartments
hic <- getCompartments(hic, chromosomes = c('XV', 'XVI'))
# Compute insulation scores and borders
hic <- refocus(hic, 'II:1-300000') |>
zoom(resolution = 1000) |>
getDiamondInsulation(window_size = 8000) |>
getBorders()
Input: A HiCExperiment object.
Output: A HiCExperiment object updated with compartments, insulation scores, and domain borders.
