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My notes for the first paper:
- Peak calling with ChIP-seq data comes with an issue of identifying candidate peaks (which ones denote a tf binding sites vs. those that are "experimental noise", or s…
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Dear TOBIAS,
How can use your tool without a motif database?
Eg, BINDetect (or another, more appropriate module) with no --motifs parameter.
Why? I'm interested in identifying, mapping and scor…
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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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To dock ligands in an active conformation protein model would involve:
- Do a positional homology based on the active OR51E2 model;
- If there is a TMR6-EXR2 salt bridge, engage it;
- Soft-pocket…
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- suppression of host MAPK signaling pathway
- induction by symbiont of host MAPK signaling pathway
also, change label of 'pertubation of host innate immune response MAPK kinase signaling' to ju…
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Current notebook here: https://github.com/pinellolab/DNA-Diffusion/blob/latent-space-representation/vq_vae_diffusion.ipynb
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Hello,
I successfully run the scripts on my genomes. It might be heplful if you add a linked to your Collection of Position Weight Matrices in the ReadMe file and a description of the cluster buste…
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Hi,
I am trying to validate whether I have TOBIAS working. Are there test output files / figures for the test data that can be used to validate whether my code is working?
Niko
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Hello,
Thanks you for making very useful tool, I have question regarding excel and text file crated from BINDetect step, Is it possible to filter the "diff_results" files with only entries of TFs/…
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