Hi-C Data Visualization with HiPiler (original) (raw)

Exploring Many Hi-C Features
Through Vi...")
Benjamin Bach, Peter Kerpedjiev, Nils Gehlenborg, and Hanspeter Pfister ... and special thanks to N. Abdennur, B. Alver, H. Belaghzal, A. van den Berg, J. Dekker, G. Fudenberg, J. Gibcus, A. Goloborodko, D. Gorkin, M. Imakaev, Y. Liu, L. Mirny, J. Nübler, P. Park, H. Strobelt, and S. Wang for their invaluable feedback during the development of HiPiler.

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Simple to use
No comparisons
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Highly flexible No interactions Time consuming Rao et al. “A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.” Cell, 159(7):1665–1680, 2014. Compare thousands of features Use metadata Find subgroups Inspect aggregates Interactive

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Interactive Exploration of Many Hi-C Fe...")

←
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Assessing individual, average, and ...")

Correlation of features ...")

Interactive Subgroup Explora...")

files in
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files in
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  1. Open hipiler.higlass.io. Done
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Level server coords pVal _group 22 25000 45000 + 22 25000 45000 + rao- gm12878 -14 2 higlass.io hg19 0.897 WT 22 25000 45000 + 22 25000 45000 + rao- k562-14 2 higlass.io hg19 0.833 T1 17 25000 45000 + 21 125000 145000 + rao- gm12878 -14 1 higlass.io hg19 0.971 L1 BEDPE TO CSV REQUIRED USEFUL NUMERICAL _CATEGORICAL

Level server coords pVal _group 22 25000 45000 + 22 25000 45000 + rao- gm12878 -14 2 higlass.io hg19 0.897 WT 22 25000 45000 + 22 25000 45000 + rao- k562-14 2 higlass.io hg19 0.833 T1 17 25000 45000 + 21 125000 145000 + rao- gm12878 -14 1 higlass.io hg19 0.971 L1 BEDPE TO CSV REQUIRED USEFUL NUMERICAL _CATEGORICAL Defined by you From higlass.io (or your own instance)

(in about one week...)
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View Config
{
"fgm": {
"fragmentsServe...")
[ ... ], "fragmentsDims": 20, "fragmentsPercentile": 100, "fragmentsPadding": 0, "fragmentsIgnoreDiags": 0, "fragmentsNoBalance": false, "fragmentsPrecision": 2, "fragmentsNoCache": false, }, "hgl": { ... } }

View Config
{
"fgm": { /
/ Defines sni...")
view "fragmentsServer": "http:/ /higlass.io/", "fragments": [ ... ], "fragmentsDims": 20, "fragmentsPercentile": 100, "fragmentsPadding": 0, "fragmentsIgnoreDiags": 0, "fragmentsNoBalance": false, }, "hgl": { ... } / / Defines HiGlass view }

View Config
{
"fgm": {
"fragmentsServe...")
/ HiGlass server "fragments": [ ... ] / / BEDPE-like loci "fragmentsDims": 20, / / Number of bins "fragmentsPercentile": 100, / / Upper percentile capping "fragmentsPadding": 0, / / Padding relative to loci "fragmentsIgnoreDiags": 0, / / Num. of ignored diagonals "fragmentsNoBalance": false, / / Cooler balancing }, "hgl": { ... } }

JSON
ARRAY
REQUIRED
NUMERICAL
_CATEGORICA...")
"strand1", "chrom2", "start2", "end2", "strand2", "dataset", "zoomOutLevel", "corner-score", "U-var", "L-var", "U-sign", "L-sign", "_group"], ["22", 17425000, 17545000, "+", "22", 17425000, 17545000, "+", "rao-gm12878-1kbmr", 1, 0.91491, 0.061801, 0.033795, 0.60558, 0.6278, 1], ["22", 17555000, 17645000, "+", "22", 17555000, 17645000, "+", "rao-k563-1kbmr", 1, 0.89306, 0.035257, 0.020245, 0.54321, 0.69136, 1], ... ] HEADER LOCI

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