User: Shicheng Guo

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Shicheng Guo7.3k
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Posts by Shicheng Guo

<prev • 515 results • page 1 of 52 • next >
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Polygenic Risk Scores for Lung Cancers
... Anyone have the candidate SNP list for Polygenic Risk Scores estimation for Lung Cancers? Thanks. ...
lung cancer prs written 20 days ago by Shicheng Guo7.3k • updated 5 days ago by Biostar ♦♦ 20
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Genotyped SNPs were lost after michigan imputation server imputation and phasing
... Hi All, I run a imputation and phasing with 'michigan imputation server' for exom-beadchip array data and I found some of genotyped SNPs in the exom-chip were lost in the output file. Is it common or I made some mistake in the option selection or others? Thanks. ...
imputation michigan phasing written 4 weeks ago by Shicheng Guo7.3k
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Comment: C: Looking for Population Genetics Simulation Software
... any updates after 2.2 years? ...
written 5 weeks ago by Shicheng Guo7.3k
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... Hi ATpoint, How to apply Aspera in Linux server? ...
written 5 weeks ago by Shicheng Guo7.3k
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Answer: A: How To Convert Snp Genotype Data Into 0,1,2 Matrix
... How about `Generate_SSD_SetID` function in `SKAT` R package? library("SKAT") SKAT.input<-Generate_SSD_SetID(File.Bed, File.Bim, File.Fam, File.SetID, File.SSD, File.Info) SSD.INFO<-Open_SSD(File.SSD, File.Info) SSD.INFO$nSample SSD.INFO$nSets Result.SKAT<-SKAT.SSD.A ...
written 6 weeks ago by Shicheng Guo7.3k
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Comment: C: How To Convert Snp Genotype Data Into 0,1,2 Matrix
... Missing genotypes can be imputed advance to avoid un-expected error. ...
written 6 weeks ago by Shicheng Guo7.3k
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Comment: C: Finding SNPs in LD with GWAS hits
... The SNAP application has been taken down due to a lack of resources to support it and because the data sets used were increasingly dated since 2017 ...
written 8 weeks ago by Shicheng Guo7.3k
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Answer: A: Relatedness software for 20,000 exome sequencing datasets.
... Only select tag-SNPs and run the relatedness2, the less SNPs you use, the faster it is. ```plink --vcf input.vcf --indep-pairwise 50 10 0.8 --recode vcf --out output ``` the third parameter 0.8 is R2 threshold. you can try 0.6 0.5 or different values to control the number of SNPs. `plink` is a sof ...
written 9 weeks ago by Shicheng Guo7.3k
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Answer: A: Simulate genotypes based on reference genotypes with same LD structure?
... Simple bi-allelic SNPs without structure: `PLINK` Coalescent approaches: `GENOME` Forward-time approaches: `MetaSim` and `simuPop` Resampling approaches: `Hapgen2` ...
written 9 weeks ago by Shicheng Guo7.3k
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Answer: A: simulate genotypes for SNPs, considering MAF and LD structure
... Simple bi-allelic SNPs without structure: `PLINK` Coalescent approaches: `GENOME` Forward-time approaches: `MetaSim` and `simuPop` Resampling approaches: `Hapgen2` ...
written 9 weeks ago by Shicheng Guo7.3k

Latest awards to Shicheng Guo

Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: How to change the default fold of the downloading sra data using prefetch ?
Appreciated 4 days ago, created a post with more than 5 votes. For bedGraphToBigWig Tutorial and Report
Popular Question 12 days ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 28 days ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Multiplex PCR Primer Design Tools
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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Great Question 7 weeks ago, created a question with more than 5,000 views. For Good Habit for Bioinformatics Analyst or Scientist
Great Question 7 weeks ago, created a question with more than 5,000 views. For fastq-dump split-spot and skip-technical
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: error in running R
Student 8 weeks ago, asked a question with at least 3 up-votes. For Definition and formula of methylation heterogeneity
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: error in running R
Great Question 9 weeks ago, created a question with more than 5,000 views. For fastq-dump split-spot and skip-technical
Scholar 9 weeks ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: error in running R
Student 11 weeks ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Student 3 months ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: error in running R
Appreciated 3 months ago, created a post with more than 5 votes. For A: What is a typical workflow to correlate methylation and expression data?
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10

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