issues Search Results · repo:JianYang-Lab/gsMap language:Python
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inJianYang-Lab/gsMap (press backspace or delete to remove)Hi gsMap authors, My GWAS summary statistics are based on the GRCh38 genome assembly. I noticed that the gsMap_resource
folder you provided is built from GRCh37. Can I still use it with my data? If not, ...
EddyWu144
- 4
- Opened yesterday
- #87
Dear Team, thank you again for providing such excellent tools. I have been testing them across about 98 traits, and the
results have been quite reasonable for several of them. I have a question regarding ...
TheSingleCell
- 2
- Opened 2 days ago
- #86
EddieLvThank you for developing this excellent tool! I have a quick question regarding the formatting of summary statistics
tables that do not include a sample size ( N ) column for each variant, which is often ...
- 2
- Opened 7 days ago
- #84
Dear team, Awesome work! Just a quick question: If my summary stats file is from a GWAS study on European ancestry, I
can directly use the resource files you provided in the tutorial, is this correct? ...
- 2
- Opened 8 days ago
- #83
Dear Developer,
First, thank you for developing this powerful tool and providing such clear tutorials. I’ve been following the workflow
to analyze my own dataset, but I’ve encountered a question regarding ...
bug
LiuJiamao521
- 2
- Opened 9 days ago
- #82
Hello, when I run gsMap in a cluster (headless rocky linux operating system) I get this error:
_BrowserFailedError( choreographer.browsers.errors.BrowserFailedError: ( The browser seemed to close immediately ...
bmateosa
- 2
- Opened 10 days ago
- #81
Dear Author,
I would like to run the training without using --annotation for supervision, but I have tried various methods without
success:
Omitting the --annotation argument: The command fails with ...
seasonzhao
- 2
- Opened 21 days ago
- #79
Describe the bug Hi, when I try following the Data Format part of the tutorial, I find that the example dataset of
HEIGHT is not accessible. Do you know how this happen?
To Reproduce
wget https://portals.broadinstitute.org/collaboration/giant/images/4/4e/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.gz ...
bug
wurucheng123
- 3
- Opened 23 days ago
- #78
Hi developers,
First, thank you for this great tool! I noticed that gsMap uses spatial transcription data and ABC/Roadmap enhancers to
link SNPs to genes(in Use Enhancer-Gene Linking way). For cases where ...
enhancement
- 2
- Opened 24 days ago
- #77
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