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Hello, msbentsen,
I have some questions when using **TOBIAS** for my ATAC-seq data analysis, I read the docs on TOBIAS Github, but still confused.
My atac-seq analysis propose is finding different T…
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Hi, thanks for developing SQANTI3 for Isoseq data analysis! I have some issues with generating the report after running sqanti3_qc.py. I didn't get the report but other output files seem normal. The f…
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Hello,
I was hoping someone could help me set up VAME on Colab. I am new to VAME and coding altogether, but I tried my best to figure it out. I am aware this question has been asked in #47 and I ha…
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Hi,
When running addMotifAnnotations to an ArchR project, is it possible to add both 'core' and 'unvalidated' collections from JASPAR2020 database? When I run:
Multiproj
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Hi. It looks like I am running into issues with DNA motif analysis and specifically when I use the function add motifs(). I would really appreciate some feedback or help on this issue. Thank you f…
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We had this figure, then it was taken out again, and we still need it (probably as supplementary).
What's happening and how are we we going to fix it?
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Dear Egor,
Sorry to interrupt you again. I still hope to ask for four more questions about EHdn.
1. The table shown below is the result for outlier locus analysis. I noticed that some counts in …
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Hi!
i was wondering, if i include two different ranking databases during the pySCENIC ctx step, which have either 10kb UP and down of TSS or 500bp up and 100 down annotations, then does pySCENIC in…
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Hi Mette,
Thanks for developing this tool, we are very interested in bringing this analysis into more of our scATAC workflows! While hoping to optimize for running time, I found the --track-off opt…
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1. Add example experiments to a new user (see add_example_experiments.py, and also #111 )
2. Add message:
```
We have just created you an account on www.ms2lda.org where you can explore some prev…