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Dear authors:
I am using autoAugTrain.pl to train a new model for a reference genome, but I met an error:
"augustus: ERROR Properties::getProperty(): cannot convert value "#" of key "/Constant/opalp…
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Hi,
I was trying to get predictions from the code which is published in this GitHub repo.
However, the predicted scores are slightly different from the one predicted by the website.
The predictio…
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Hello,
I just downloaded and installed CONSTAX into a new conda environment. It seems there are some out-of-the-bag dependency issues (or incomplete installation, perhaps?) and a weird syntax warning…
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Hi there,
Thanks for your work with DeepVirFinder. I've been trialing it with some environmental metagenome data, but was also interested in whether it would be appropriate for use with identifying…
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I've described the project to a few ppl now, and one question that comes up is as follows:
- There is little dispute that higher order models for predicting TF-DNA binding are more capable than si…
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Hi Ruchir,
Thank you so much for such amazing work! This is very helpful. I'm wondering if I can get some clarifications on `analysis/all_gene_perf.csv`?
1. Are the Pearson correlation shown fr…
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Hello Jared,
I'm new to Nanopolish but would like to use your software for detection of RNA's native structure, similar to SHAPE-map presented during London Calling 2019. Recently, generated two se…
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## ❓ Questions and Help
I have pretrained roberta-base on dna promoter sequences of plants (working on a project). I am currently trying to finetune it on a downstream task of predicting gene express…
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Hello,
I just read your paper about silencer database, and noticed that you implemented CNN to predict silencers. Would you like to explain how to run `DeepSilencer`? What file does `DeepSilence…
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**EDIT I guess it would help if I were to read the publication to see especially the figures on time and amplitude domains' effects on base identity.**
Hi, thank you very much for developing this t…