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Hi,
I tried running SEACR and Macs2 on my CUT&Tag data using different parameters。The following table 1 were the results that SEACR with or not with IgG sample S42, norm or non parameters。I am con…
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### 🐛 Numpy module works fine with Torch modules, but not TorchScript.
```python
from scipy.signal import find_peaks
batch_size = 1
input_data_shape = 1000
input_shape = (batch_size, input_da…
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If using smoothing the graph is cut-off, when peaks lead to min or max values.
This can be circumvented by artifically lowering the domain's min and increasing the max.
The problem is that manipu…
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TODO
- [ ] migrate code to download data elsewhere in cooltools (e.g. lib.io)
Notebooks:
i/o
- [ ] #6
pairtools-walkthrough:
- [ ] map
- [ ] parse
- [ ] sort
- [ ] dedup
- [ ] stats
…
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This is related to issue #375 . Basic functionality is implemented with the `reconstructChromPeakSpectra`. This function assigns all MS2 chromatographic peaks to an MS1 chromatographic peak if the cor…
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just putting it out there because we discussed it a bit with johannes, but a lot of function exist for accessing peaksData:
- accessor function : `rtime()`
Usefull for `do.call()` or `|>` (I gu…
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Hi,
I just encounter a problem of finding specific peaks or troughs in a signal, and can't find appropriate functions in Julia.
In MATLAB, the `findpeaks` is very convenient that it could find l…
babaq updated
4 years ago
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I am using SEACR for CUT&RUN data.
For one of my target + control datasets, I am getting a zero bytes output bed file (norm option). When I run the two files independently (non option), I get be…
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I am following the steps in [https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands](https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands).
…
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Hi Tao,
I used INPUT as my ctrl and used default parameters to call narrow peaks.
I encountered a warning:
Since the d(171) calculated from paired-peaks are smaller than 2*tag length, it may be i…