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Hello,
I have a question on the matrix normalization.
Although in your paper, you have clearly stated that "(existing methods) is fundamentally flawed, because the inherent biases present in the…
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I am trying to plot TADs I called on a Hi-C matrix with resolution 1kb. But no contacts are being plotted on the map. This is my command:
`hicPlotTADs --tracks tracks.ini --region chr01:6800000-85000…
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I wasn't able to clearly understand this from the documentation.
If I have a loop file (bedpe) with the format: chr1 start1 end1 chr2 start2 end2
can I use that file directly into the --bed argum…
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Hi @njdbickhart ! Awesome tool. When I run the wrapper script, I get a bunch of "Error parsing malformed sam at record: " errors. Otherwise, everything seems normal and I get the expected outputs…
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Hello,
Thanks for this new tool. I am attempting to run diffDomain using the command `python diffdomain-py3/diffdomains.py dvsd multiple input/h9_merged_30_25kb_25000.cool input/smpc_merged_30_25kb_…
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Hi, I have noticed that HiGlass is running slow these days. I used to be able to navigate smoothly before. What could be the reason?
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Hi everyone,
I hope you're all fine.
I noticed that **hicConvertFormat** won't return negative values that are still present in a given .h5 matrix (norm KR).
This matrix represent differential in…
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IUC has quite some tools using datatypes that are not known to Galaxy:
```
for i in $(grep 'format="' . --include "*xml" -r | sed "s/'/\"/g" | sed 's/.*format="\([^"]*\)".*/\1/' | sed 's/,/\n/g' |…
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hi yufanzhou
your method is very useful . but i have a little question. the juicer's result, like "resule.hic", whether it can be deal with HiSIF.
if it can , how shou i do ?
i will …
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Hi,
I'm using `hicexplorer: 3.7.2; pyGenomeTracks: 3.8; numpy.version: 1.26.4; Python: 3.9.12`, to run hicDetectLoops to call loops, got error copmplain that `np.float` was a deprecated alias for …