2. Input for the locally running version

If you'd like to use the locally running version of PredCID, the inputs requires the position information of indels both in cDNA and genome, which can be annotated by the tool TransVar. For the selection of various options in TransVar, please see the figure below.

When you obtain the position information of indels both in cDNA and genome, a two-column file could be input into the locally running version as below.

3. Quick start for the locally running version

The following shows the demo code of PredCID.
Please feel free to contact us if you need any help: zhenyuyue@ahau.edu.cn

getResults("example","outputFileName")#example.csv is a file containing frameshift indels.

4. Outputs

In general, the predictions are done on the fly, and in seconds to minutes, depending mainly on the size of the input data. Users will receive an email attached with the result file. For each input, the model returns a score between zero and one, where indels with higher scores are more likely to be driver frameshift indel. Here, the indels with scores greater than 0.5 are predicted as drivers.