What datasets are available out there for prediction based on DNA sequences? I am looking for publicly available data for a genomics deep learning project. My goal is to compare different architectures to predict biological insights from DNA sequences.
I have heard about Janggu before, but I am looking for a few datasets which are like the MNIST equivalents in genomics. Kaggle doesn't seem to have many such datasets, and I would be happy if you share your insights about potential datasets that one could use.
For example, it could be datasets that map 100-Mers to their ChIP-seq values or datasets that annotate a DNA sequence with the probability that a transcription factor would bind to it.
Choong and Lee lists a few datasets on their IEEE paper from 2017:
Good question and the Janggu link is cool. Thanks!
Kaggle is/was heavily image recognition. There isn't an MNIST type data set in genomics, in case anyone is wondering this is a classic natural language processing (NLP) type analysis to identify handwritten single digit numbers.
There has been several FDA precision challenges, one being described here:
FDA precision challenges
This could provide something towards a 'standard'.
A key issue remains the accurate vectorisation of sequence and whether you think that is/was satisfactory in my personal opinion.
There is an old review article here