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I noticed that you have a script called get_SNP_STR_LD.v2.py for calculating linkage disequilibrium (LD) between str and snp. Could you provide an example format for the str? I happen to be dealing wi…
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When I made the locuszoom plot, I found that there was no LD information of the locus in…
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Hi Doug,
I'm currently using LDAK (Version 6) for my analysis, and I've encountered an error that I'm struggling to resolve. Here are the details of the issue:
```
-- -- -- -- -- -- -- -- -- -- -- …
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- Outlier detection
- SNP/environment
- Linkage disequilibrium methods
- Neutrality tests
## By marker type:
- [x] SNP
- [ ] Sequence
- [ ] Microsatellite
Please refer to the issue number when submit…
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I would like to start generating some real examples of packages
if @Ilia-Kosenkov and @clauswilke could help.
We could, for example:
* Show memory mapped files with parallel parsing (such as JS…
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Hi, I am trying to add the non-linear regression tendency line to the Linkage Disequilibrium (LD) plot. I followed the manual document of PopLDdecay and got the plot. However, I am looking to make plo…
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Hi
I am trying to generate polygenic scores using PRSice v2 **without phenotype data for the target population**. i.e. I just want to use the GWAS summary statistics (and specifically the effect si…
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I'm wondering that the meaning of R2 in stat model based on a bed file.
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Circuitscape borrows algorithms from electronic circuit theory to predict connectivity in heterogeneous landscapes. Landscapes are represented as conductive surfaces, with low resistances assigned to …
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ConPair software uses 7387 pre-selected informative genomic markers based on following criteria.
SNVs (easier to genotype from sequencing data)
exonic (to allow comparison of exome and WGS samples…