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QData / DeepChrome

Bioinformatics16: DeepChrome: Deep-learning for predicting gene expression from histone modifications
http://deepchrome.net
Apache License 2.0
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dataset clarity #3

Closed purvanshi closed 5 years ago

purvanshi commented 6 years ago

Hello, Could you please provide a detailed readme of how the data was generated. I referred to #2 but its still confusing. Proper steps would be beneficial for all. Could you please explain the toy data. I understand from the paper that 5 five selected histone modifications from REMC were used as x and the output of gene expression (+1/-1) as y. I couldn't find the column labelling anywhere(which column denotes what and which column is the output).

Thanking you in advance. Purvanshi

rs3zz commented 6 years ago

Hello Purvanshi,

I apologize for the delay. I somehow missed seeing this comment. The column labels are as follows for the toy dataset - GeneID, Bin Number, HM1, HM2, HM3, HM4, HM5, Label. Here HM= Histone Modification and HM1=H3K27me3, HM2=H3K36me3, HM3=H3K4me1, HM4=H3K4me3, and HM5=H3K9me3.

As far as data generation steps are concerned, I will try and write a more detailed readme. Meanwhile, is there anything specific you are confused about?

Regards Ritambhara