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Hi
The STAR version I used is 2.7.11a
and the code is
```
STAR --genomeDir $REF_DIR \
--readFilesIn $OUT_DIR/${READS}_1_trimmed.fq $OUT_DIR/${READS}_2_trimmed.fq \
--outSAMtype BAM Sort…
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Current impl of `annotate_reactome.py` requires access reactome.org website.
Reactome IDs -> Pathways titles annotator could use cached databases downloaded from rectome.org: `/mnt/stripe/bio/genomes…
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Hello authors:
Recently i studied your work about this mRNA-miRNAs-cancer-pathways.
But there are some points i didn't understand.
1. You calculated the correlation between miRNA and its target mR…
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Hello,
I would like to request that the tables used by GEMINI's built-in analysis tools be added into VCF2DB.
Ideally, all tables that are default loaded with the command:
$ gemini load
that…
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For a few months, I've struggled with getting this method to work (first issues relating to getting geneset names that later resolved itself, and now issues with getting the actual genes in the genese…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/Lu-Group-UKHD/SmartPhos
Confirm the following by …
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Excuse me, I am trying to add 2 IRL in the LRI_curated, but I don't know how to find the matched GO and KEGG ID, which can be added in the LRI_curated_GO and LRI_curated_KEGG. Can you tell me how to r…
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Dear Joelle
We're using Regenie to perform standard gene-level analyses (burden, skato etc) from population-scale WES data.
We'd like to begin exploring testing entire pathways using the same me…
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Adjust score to reflect the adjacency of two proteins connected by an edge (in some cases we connect two proteins that are actually linked via one or more intermediary proteins). See David's annotatio…
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### Expected behavior
Select json code from existing cohort pathway (17 in production) and open new cohort pathway in beta, navigate to utilities and select existing json code delete it and use ctrl …