NeoLoopFinder

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Can I use NeoLoopFinder for other organisms?

1

This software is really cool. Can you extend to other organisms?

xinghua1001

NeoLoopFinder for Micro-C

4

Hi Xiaotao, Thank you very much for this wonderful tool. Does NeoLoopFinder apply to MicroC data? And "uniform" should be selected for "-e" parameter? Thank you, Pinpin

PinpinSui

Numpy.int AttributeError

1

The following line raises an attribute error for new versions of numpy: https://github.com/XiaoTaoWang/NeoLoopFinder/blob/b7587c90d1f20383b62a96f8281e4ba397101a98/neoloop/callers.py#L822 Error message: ``` AttributeError: module ‘numpy’ has no attribute ‘int’. `[np.int](http://np.int/)` was a deprecated alias for the...

TeoSakel

Color of interaction matrix

2

Hello, I have been unable to figure out how to change the color ramping for the interaction matrix. Is there a way to modify the python code you have provided...

stanleyrc

download pre-trained Peakachu models

8

Hi Xiaotao, Our sever is offline. Would be possible to download all pre-trained Peakachu models for neoloop-caller locally? I tried the https://dl.dropboxusercontent.com, but it seems not accessible. Thank you. Bo

Bo-UT

CNV segmentation crash

11

Hi @XiaoTaoWang When running the `segment-cnv` module, I keep running into the error below. When running at 10kb, the CNV profile was full of 0's, and I got this error...

cmdoret

AttributeError: module 'rpy2.robjects.numpy2ri' has no attribute 'numpy2ri'

4

Dear author, Thanks for developing this package. I am trying to run calculate-cnv but did not get through. The two issues I met: (1) bw.stats does not accept np.int so...

YuanlongLiu

Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder?

4

Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder? I prefer to simple or linux command line format.

wzhang42

neoloop-caller failed

3

when i run neoloop-caller: neoloop-caller -O M1.neo-loop.txt -H M2_5000.cool --assembly M2.assemblies.txt --no-clustering --prob 0.95 the error: --2022-09-09 23:00:38-- https://dl.dropboxusercontent.com/s/5nnxf9drw39acu5/high-confidence.50million.5kb.pkl?dl=0 正在解析主机 dl.dropboxusercontent.com (dl.dropboxusercontent.com)... 66.220.147.11, 2001::766b:b4d8 正在连接 dl.dropboxusercontent.com (dl.dropboxusercontent.com)|66.220.147.11|:443... 失败：连接超时。 正在连接 dl.dropboxusercontent.com...

yangfeizZZ

Triangle fails to plot some off-diagonal contacts

3

Possibly related to https://github.com/XiaoTaoWang/NeoLoopFinder/issues/6#issuecomment-884874868 . I successfully called neoloops in my sample using neoloop-caller. Adapting code from this repo's readme, I generated a Triangle plot of my region of interest,...

auberginekenobi