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我是一名学生，想要复现文章的代码，我按照代码中的注释使用 BrainGNN_Pytorch 项目中的 01-fetch_data.py 下载了 ABIDE 数据集的 pipeline: cpac，atlas: ho 的数据，将下载的数据放在了 ./input/data/ 文件夹，我将 Phenotypic_V1_0b_preprocessed1.csv 中创建了 Group 列，等于 DX_GRO…
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Reviewing our PhenotypicFeature profile and related content. This issue is to track and discuss anything while we review the current modeling of a phenotype. This first post can be considered a wiki…
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On Slack, @colleenXu pointed out that it might make more sense for "Neoplastic process" ([T191](https://uts.nlm.nih.gov/uts/umls/semantic-network/T191) or tree number B2.2.1.2.1.2) to be classified as…
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The counts reflect the number of session matching the query, not the total per subject, so we should update the column names in the results TSVs to avoid confusion (the API results also include "match…
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Show how to plot a figure with counts of phenotypic features per sample.
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- Create a bag of phenotypes
- Do something with this bag:
- Create a phenopacket
- Run phenogrid for one of three reasons
- Identify phenotypically similar genes
- Identi…
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Allow users to visualize a Phenogrid, with a Phenopacket (json or other formats) as input.
Ideas: this could be an additional option in the step where users can select a phenotypic profile (list of…
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Hello,
I am wondering if there is any information on the package used to create phenotypic distribution graphics that show allelic differences at significant SNPs. I have not been able to find inf…
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For correctness of the results, we should ensure that all analyzed phenotypic features are descendants of Phenotypic abnormality.
This check is best done at the time when `Sample` is created. We must…
ielis updated
10 months ago
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At the moment, we have tests which check that:
- A custom `PhenotypicSession` called `ses-unnamed` is created by the `bagel pheno` command when it receives a phenotypic TSV with missing session column…