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Hi Xindong,
I am confused by the mean_position in cistromeDB (http://cistrome.org/db/#/). The QC motif page for specific ChIP dataset demonstrated a mean_position always less than 0. Does that mean t…
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When running a fresh conda install of Ananse (so the master brench), it crashes on binding. I'm checking (in a bit) which package is different between my old 'master conda env' and the newly generated…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ManchesterBioinference/Motif2Site
Confirm the fol…
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https://mp.weixin.qq.com/s/pN4qWdUszuGqr8nOJstn8w
ixxmu updated
2 years ago
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Hello,
Thank you for this great tool.
I have trained two models for TF1 and TF2 in cell line A and predicted TFBSs for the whole blood lineages, such as HSC, CMP, GMP, etc. In cell line A, I ha…
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Hi Mette,
Thank you very much for providing this fantastic tool for ATAC-Seq footprinting. However, something strange happened when I was doing my analysis. Two motifs which I am interested were h…
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https://mp.weixin.qq.com/s/zt-5JshP71ZX3OwPOsfagA
ixxmu updated
2 years ago
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Hello Dr. Sidhom,
I recently came across your “DeepTCR” paper and I found the idea of combining supervised and unsupervised learning and applying them to modeling TCR repertoires intriguing. Also, …
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using GRCz11 with a pfm file obtained from `gimme motif2factors`, nearly none of of the TFs are found.
excerpt from the log:
```
2021-11-03 20:37:31 | INFO | Using FOXK2 model for foxi1
2021-11-…
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Greetings everyone,
In the paper, you mentioned that to get promo-regions prediction, TF-binding motifs and variants prediction outside coding regions, the DNABERT-XL was used, which takes sequence…