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Just time to open an issue about this so we can track it better.
We've discovered that the GraphQL endpoint gets stale and starts to not work intermittently, which makes the bedbase.org server unre…
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Nice tool, congratulations! I would like to use it on 10x ATAC/multiome data. Could you please explain the following?
1. It would be great to see an example of how to start from `fragment.tsv.gz` s…
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Hi,
I have a couple issues with the `getPrecomputedBias()` function.
First, it's a bit confusing that the path to the h5 bias file is hard-coded, I had to edit getBias.R to make it work for my …
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Hello,
what is the input file (**--coord TEXT Path to stripe coordinate table**) for stripenn score? is it the **result_filtered.tsv**?
Best,
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Hi,
Directly using the sample data in folder custom_data_files to run run_bichrom.py will result in an error message as follows:
```python
python run_bichrom.py -training_schema_yaml ../custom_da…
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Hi,
I have been using TOBIAS as part of my research project, and it's been a great tool.
I ran TOBIAS ATACorrect and ScoreBigwig on about 50 or so bam files, and plotted the FP score distributi…
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Hi,
Sorry I have to open a new issue even I just had opened a issue (#1441 ) several days ago.
I have downloaded the [multiome scRNAseq and scATACseq data](https://www.ncbi.nlm.nih.gov/geo/query…
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Hello,
I have previously used demuxlet successfully to demultiplex single cells and call doublets from 4 homozygous SNP lines in Drosophila using the known SNPs for each line. Now the same lab has a …
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Hey thanks for the package. I was reading the dictys paper on bioarxiv and it says
To reconstruct a context specific GRN for each group of cells, Dictys first infers TF binding sites in regulato…
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Hi there,
Thank you for developing and maintaining this tool. I was wondering if using only Nfr fragments would improve the performance. Also, is there any minimum read # / library recommendat…