Hi all,
I am currently looking to validate a pipeline I have created that involves using Cox models. I have used TCGA bulk RNA-Seq-datasets. Unfortunately, I also need to use another data source besides TCGA to complete the project. I am having difficulty finding cancer datasets that meet the following requirements:
- Normalized (TPM/FPKM) bulk rna-sequencing data from various cancers
- Contain vital status (e.g. alive or dead)
- Contain followup information (e.g. how many days did a patient live during the study)
- Dataset that is not from TCGA
- Contain patient information
I have been able to get close finding datasets that contain patient information, normalized sequencing data, and survival status that is not from TCGA, but it lacks followup time which is a requirement for survival analysis (Cox models).
Thanks in advance!
1 answer
How about using the data from the GEO database, you will surely find the datasets from there according to your requirement.
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You can try cBioportal https://www.cbioportal.org/ which has patient information.