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[
{
"url": "http://higlass.io/app/?config=L4nKi6eGSzWOpi-rU2DAMA",
"title": "Epilogos",
"description": "The epilogos track type (https://epilogos.altiusinstitute.org/) shows an overview of the epigenetic states found along the genome.",
"category": "Useful view configurations",
"image": "https://user-images.githubusercontent.com/2143629/42416058-b698b002-8232-11e8-9952-b43108cfdbd2.png",
"columns": 2,
"locations": ["chr3:180,376,342-180,443,561 & chr3:180,405,434-180,415,676 [offset 0,0:0,0]"]
},
{
"url": "http://higlass.io/app/?config=MSHhOBbOSW6iIovB5yk6BA",
"title": "HiC Data vs. Maps",
"description": "Maps of earth and HiC data have features across a similar range of scales. This view configuration shows them side by side with linked zoom scales.",
"category": "Useful view configurations",
"image": "https://user-images.githubusercontent.com/2143629/28455807-962ed2b6-6e00-11e7-9c00-3c967c385027.png",
"columns": 2,
"locations": ["chr17:46,544,763-46,670,212 & chr17:46,580,119-46,662,543 [offset 0,0:0,0]"]
},
{
"url": "http://higlass.io/app/?config=OPPFtzbuR76vtUIshTEOGA",
"title": "Comparison of different balancing methods (VC, KR, and ICE)",
"description": "Three different methods of balancing HiC data. The original matrix is from IMR90 cells profiled using dilution HiC as described in Rao et al (2014)",
"category": "Paper figures",
"image": "https://user-images.githubusercontent.com/2143629/28230569-86e5d160-68b5-11e7-8ee2-045534e43431.png",
"columns": 1,
"locations": []
},
{
"url": "http://higlass.io/app/?config=IPCHmdOQR4CDY2sqj5VJHQ",
"title": "2D TAD caller comparison (Forcato et al 2017, Fig. 3)",
"description": "A comparison of the outputs of different TAD callers for Replicate H of Rao et al GM12878, as reported by Forcato et al. 2017 (Fig. 3). TAD calls were lifted over from hg19 to hg38.",
"category": "Paper figures",
"image": "https://user-images.githubusercontent.com/2143629/28928936-9ede74e8-783c-11e7-9dc4-e8221fbec728.png",
"columns": 2,
"locations": ["chr1:152,901,103-156,043,982 & chr1:152,791,350-155,757,787 [offset 0,0:0,0]"]
},
{
"url": "http://higlass.io/app/?config=JALHH-HzQGeJCaJaU9EwTA",
"title": "TAD caller comparison (Forcato et al 2017, Fig. 3)",
"description": "A comparison of the outputs of different TAD callers, as reported by Forcato et al. 2017 (Fig. 3). The heatmaps show the combined data from all replicates for GM12878 MboI. Each view contains the calls produced by one caller while each row shows the calls for a single replicate.",
"category": "Paper figures",
"image": "https://user-images.githubusercontent.com/2143629/27559759-baa70a02-5a8f-11e7-93dc-eefcedfbefd5.png",
"columns": 2,
"locations": ["chr10:71,767,583-89,043,852 & chr1:1-1 [offset 0,0:-77628426,-74054026]"]
}
,
{
"url": "http://higlass.io/app/?config=Tf2-ublRTey9hiBKMlgzwg",
"title": "Figure 1 from HiGlass paper (Kerpedjiev et al 2017, data from Schwarzer et al 2017)",
"description": "An illustration of the cohesin-dependent fragmentation of compartments as described by Schwarzer et al. (2017)",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/24535688/a6043f1a-15a3-11e7-8197-d5d3ce227bc6.png",
"columns": 1,
"locations": []
}
,
{
"url": "http://higlass.io/app/?config=Q5LdNchQRLSZ_0yKsTEoiw",
"title": "Figure 2 from HiGlass paper (Kerpedjiev et al 2017, data from Schwarzer et al 2017)",
"description": "A composition for exploring and comparing details in two different conditions.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/24535699/b47986a4-15a3-11e7-9589-d3f26047b457.png",
"columns": 1,
"locations": []
}
,
{
"url": "http://higlass.io/app/?config=LguhdXQ3QY61fhTviF3urw",
"title": "Two independent views",
"category": "Useful view configurations",
"description": "Two independent views showing different loci (SOX2 and WISP1) in the same dataset. The zoom level and location differ between the two views.",
"image": "https://cloud.githubusercontent.com/assets/2143629/22596203/9aba54cc-e9f8-11e6-8976-b549d9b2dc82.png",
"columns": 2,
"locations": ["chr8:133,762,526-134,602,796 & chr8:133,743,009-134,581,224 [offset 0,0:0,0]"]
},
{
"url": "http://higlass.io/app/?config=M39Opmf5TFSpzi3odFGbYQ",
"title": "Chromosome grid",
"category": "Track expose",
"description": "The chromosome grid shows where the boundaries of the individual chromosomes lie. The boundaries are specified in a chomosome sizes file in the higlass config.",
"image": "https://cloud.githubusercontent.com/assets/2143629/22596635/54cddd92-e9fa-11e6-8994-3aa35f2a0481.png"
}
,
{
"url": "http://higlass.io/app/?config=YTNBiN7gTU-z-Z0RU24-2g",
"title": "Six linked views",
"description": "Linking six views allows for easy comparison and demonstration of variation between different cell lines.",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/22829490/e2d7850e-ef70-11e6-8c8c-4705a4597ae7.png",
"columns": 2,
"locations": ["chr8:133,095,195-135,202,496 & chr8:133,488,056-134,738,650 [offset 0,0:0,0]"]
} ,
{
"url": "http://higlass.io/app/?config=VCIcCD3AQSivEdZajrW5GA",
"title": "A lone blemish",
"description": "A single region of higher contact frequency stands out in the intra-chromosomal region of chromosome 1.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/22827490/30b2b858-ef66-11e6-9c42-075243d7b1ed.png",
"columns": 1,
"locations": ["chr1:220,192,754-236,863,461 & chr1:243,525,648-chr2:2,157,968 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=AgHaxkDFRWu3xR7WGJ8ONA",
"title": "A potential structural variant in K562",
"description": "This location shows a potential structural rearrangement in the K562 cell line. It is not present in any of the other Rao et al datasets.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/22829794/3dc32e4a-ef72-11e6-8156-c3448ba32594.png",
"columns": 1,
"locations": ["chr13:58,887,886-chr14:18,540,291 & chr13:75,681,552-chr14:4,915,553 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=CafCfq2wQtyD_BbBj6HbpA",
"title": "Zoom limited view",
"description": "Maintaining a minimum zoom level can be useful to show features which are harder to see at higher resolution.",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/22841335/2fc58914-ef9f-11e6-922d-075a20e54a6b.png",
"columns": 2,
"locations": ["chr2:70,024,841-71,598,135 & chr2:70,075,417-71,426,951 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=Wxxdw3aDTwyyx9TweoxWWQ",
"title": "Horizontal diagonal heatmap",
"description": "Heatmaps can be displayed as horizontal tracks where the heatmap's diagonal is placed along the base of the track.",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23343886/ef028cfc-fc40-11e6-8bbf-3e81b39468c0.png",
"columns": 2,
"locations": []
}
,
{
"url": "http://higlass.io/app/?config=PwGNs8hlTjK9M3rUbcXs1Q",
"title": "Exceptionally strong regions",
"description": "Regions of high contact density can be found both at the ends of the chromosomes as well as in the middle.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23365563/85b314ec-fcd1-11e6-8b64-042b0e38d05f.png",
"columns": 1,
"locations": ["chr10:42,432,837-chr12:99,810,556 & chr5:111,245,201-chr7:33,176,570 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=RAbl5b4sQGS22EH2onVKoA",
"title": "Effect of RAD21 cleavage",
"description": "Excerpt from Figure 2 of Zuin et al, PNAS 2014.",
"category": "Paper figures",
"image": "https://cloud.githubusercontent.com/assets/2143629/23412374/550c2c7a-fda3-11e6-9d8d-8565c1cc091d.png",
"columns": 2,
"locations": ["chr2:147,581,662-166,486,052 & chr4:96,433,581-101,189,034 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=czoXK8QJSvGw36t6-NlKxg",
"title": "Variable region",
"description": "This region appears to have different structures in different cell lines.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23413110/bd465ade-fda5-11e6-84de-3be2e430f94a.png",
"columns": 2,
"locations": ["chr14:81,197,287-89,791,682 & chr14:81,641,819-88,989,359 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=S1WIolKxQQGtUUo0RteSWw",
"title": "Stronger contacts between chr17 and chr19 than between chr17 and chr18",
"description": "The inter-chromosome contacts between the ends of chr17 and chr19 are nearly as numerous as those between the two ends of chr18",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23508697/ee8ee83c-ff20-11e6-8039-aa54171f5975.png",
"columns": 1,
"locations": ["chr18:65,467,009-chr19:12,497,366 & chr17:75,120,822-chr18:7,012,166 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=OwPq374bQj6pKQ97iyhXKg",
"title": "Mini-views",
"description": "Viewport projections can show what part of the map is visible in each view. In this case, the position of the left view is shown in the upper-right view. The position of the upper-right view is shown on middle-right view and the position of the middle-right is shown in the lower-right.",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23513705/fc8c276c-ff32-11e6-835c-f84d215ed3a2.png",
"columns": 1,
"locations": ["chr10:17,891,616-25,671,019 & chr10:20,111,394-25,170,931 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=Y5ZUqLeiQwmd8_Pax5BCKA",
"title": "Structural variant in GM12878?",
"description": "An unusual contact pattern in the GM12878 cell line.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23533796/ce7108e4-ff81-11e6-8d09-2ec7158622c9.png",
"columns": 1,
"locations": ["chr22:21,730,632-24,120,639 & chr22:22,264,793-23,534,636 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=CTx4k9irR8GX3EKUNevxBQ",
"title": "Weak bin",
"description": "This bin has few contacts and should have been filtered by the balancing procedure.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23554476/3f4411c6-fff3-11e6-9970-7b81c0fc91c2.png",
"columns": 1,
"locations": ["chr20:22,576,597-26,529,781 & chr20:22,855,781-26,347,699 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=A__ler6aS-eBAXwdMTIjSg",
"title": "Standout streak",
"description": "One bin with exceptionally high contact frequencies.",
"category": "Interesting locations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23714260/8fb17340-03f6-11e7-8c4a-eb2103c4e02d.png",
"columns": 1,
"locations": ["chr17:80,886,361-chr18:1,007,053 & chr9:140,929,406-chr10:389,227 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=HncLr3ySQx6t_AGlqN0zhA",
"title": "Diagonal and off-diagonal",
"description": "Higlass can display both interactions along the diagonal (cis) and off the diagonal (trans).",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23766878/88b95c36-04d4-11e7-8da6-48269ee13c90.png",
"columns": 1,
"locations": ["chr10:69,525,383-chr11:42,047,150 & chr6:154,475,044-chr7:13,411,839 [offset 0,0:0,0]"]
}
,
{
"url": "http://higlass.io/app/?config=HncLr3ySQx6t_AGlqN0zhA",
"title": "One overview and three detail views",
"description": "Three zoomed in views show telomere clustering at high resolution while one provides an overview.",
"category": "Useful view configurations",
"image": "https://cloud.githubusercontent.com/assets/2143629/23769244/ce7d88e8-04dc-11e7-9a41-e8f53b330b52.png",
"columns": 1,
"locations": ["chr7:121,951,193-chr8:24,379,308 & chr6:144,974,074-chr7:30,964,424 [offset 0,0:0,0]",
"chr8:113,606,162-chr9:28,808,918 & chr6:145,431,217-chr7:31,421,567 [offset 0,0:0,0]",
"chr8:114,455,117-chr9:29,657,873 & chr7:132,073,686-chr8:30,040,440 [offset 0,0:0,0]",
"chr7:44,697,406-chr9:37,684,460 & chr6:134,964,128-chr8:81,570,445 [offset 0,0:0,0]"]
}
]
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