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Recognising ontological phenotype terms (UMLS/SNOMEDCT/HPO) directly from free text:
https://bioportal.bioontology.org/annotator
This would give a list of suggested terms for the patient record wh…
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**Snakemake version**
7.32.4
**Describe the bug**
When attempting to integrate the use of a foreign workflow management system into Snakemake, Snakemake does not execute the rule for …
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Hi,
Ive run in to an error running the somatic filter:
```
Rscript ./GRIDSS/gridss_somatic_filter --input ERR2752450.gridss.vcf --output gridss_hq_somatic.vcf.gz --scriptdir ./GRIDSS/
No referen…
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Hi, I have a series of SvABA vcfs, and I wanted to know if it was possible to tell somehow the type of a variant, since the field "TYPE" has only one observation=`BND`. I am sure that this is somethin…
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For example:
>>> batch1 = gtex_ctrl_db[:,gtex_ctrl_db.var["tissue"] == "Pituitary"]
>>> batch1
View of AnnData object with n_obs × n_vars = 2476734 × 24
obs: 'mean', 'std'
var: 'tissue', …
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Hello, I seem to be having an issue with the germline module. I'm working on the bone marrow single cell sample provided in the GitHub. Upon running the germ line module, I can only detect a much smal…
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Request to have the same feature as in MIP/SCOUT where all possibly compound variants are uploaded when looking at one variant. Including VAF-data....
![image](https://user-images.githubusercontent…
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Similar to pathology, are there example disease groups for Cytogenetics? Like how pathology has 'brain' and 'head_neck'.
On inspecting `process.py` there is a comment saying "disease specific cytog…
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Here is one such file: https://dcc.icgc.org/repositories/files/FI743257. It is originated from EGA, we transferred to Collaboratory, but the file page only shows this file exist in Collab but not in E…
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How would someone extract the schema specific data needed in order to populate lists of all of the possible values for the pathological, and clinical values for the T, N, M, and Stage Group fields? S…