Surag Nair

RunDiffusionMaps fails with pmat

10

I'm trying to do dimensionality reduction using the `pmat` instead of `bmat`. However, the `trainRegression` function has the `bmat` hardcoded, which causes `RunDiffusionMaps` to fail. https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/utilities.R#L125-L126 There is also a...

Since the linear model here is allowed to have non-zero coefficients, I encountered cases in which the coefficient was negative. https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/utilities.R#L137 As a result the normalized jacquard distances included negative...

Wrong parameters for MACS2

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https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32 According to the [MACS2 page](https://github.com/taoliu/MACS) the settings ```--shift -100 --extsize 200``` should be used for DNase-seq/ATAC-seq data. ```--nomodel --shift 37 --extsize 73``` should be used for nuclesome-seq data.

runMagic step size hard-coded here, but also taken as input

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https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMagic.R#L61

Arguments xMin xMax for plotProfile, plotHeatmap

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Hi, thanks for this very useful tool! For my current use case, I would find it useful to also specify x-axis limits different from upstream/downstream specified in `computeMatrix`. This would...

Hi Aaron and lab I was wondering if it would be possible to call bamtobed on BAM files generated for single-cell ATAC-seq for example, which have a barcode typically as...

When few barcodes are provided in `barcode_file`, the function is very slow since it populates `barcode_dict_ref` with all barcodes, even those not in `barcode_file`. https://github.com/r3fang/SnapTools/blob/eecfa5653020b80e31eed1ae5d2b13068e17a2df/snaptools/snap.py#L784 This can simply be improved...

This is the error: `File "/home/users/surag/oak/miniconda3/envs/basepairmodels/lib/python3.6/site-packages/basepairmodels/cli/interpret.py", line 192, in data_func return [dinuc_shuffle(model_inputs[0], args.num_shuffles, rng)] + \ TypeError: dinuc_shuffle() takes from 1 to 2 positional arguments but 3 were given` Followed...