User: Shicheng Guo

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Shicheng Guo8.3k
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Posts by Shicheng Guo

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Comment: C: eQTL analysis considering P-values
... Hi Andrew, I am wondering how many eQTL from GTEx are solid and credible? 10%, 50% or 70%? Is there any way to design a study to validate and evaluate it? ...
written 16 days ago by Shicheng Guo8.3k
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CRAM to amino acid based VCF
... Hi All, I am thinking is there any pipeline can call amino acid based VCF from CRAM/BAM? Thanks ...
vcf gatk cram written 17 days ago by Shicheng Guo8.3k
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Comment: C: ANNOVAR - column description
... What about P(HI)? In addition, there are some other columns without clear information: [38] "P(HI)" [39] "HIPred_score" [40] "HIPred" ...
written 22 days ago by Shicheng Guo8.3k
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Comment: C: ExAC PLI score calculation
... I am wondering why the authors don't provide a formula? ...
written 22 days ago by Shicheng Guo8.3k
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Command to download "Height" information from UKB with ukbfetch
... Hi All, Who can share a command to download `Height` information from `UKB` with `ukbfetch`. Thanks. ...
ukb height ukbfetch written 5 weeks ago by Shicheng Guo8.3k • updated 5 weeks ago by Sam3.0k
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Formula of LOEUF: loss-of-function observed/expected upper bound fraction
... Hi All, Who can share a formula to calculate LOEUF: loss-of-function observed/expected upper bound fraction in Gnomad. Thansk. ...
plof gnomad loeuf constraint gevir written 5 weeks ago by Shicheng Guo8.3k
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How to understand Instance and Array in UKB phenotype data
... Dear All, I want to receive some help to understand Instance and array in the following context: UKBB: The standard dataset (downloadable directly by researchers) contains a record of all the bulk data-files approved, however only the data-file IDs are present rather than the actual contents of ...
array field ukb instance phenotype written 5 weeks ago by Shicheng Guo8.3k • updated 5 weeks ago by Sam3.0k
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Comment: C: plink2 bgen to vcf ukbiobank
... how large it is for ukb_imp_chr21_v3.bgen? ...
written 5 weeks ago by Shicheng Guo8.3k
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GPCR, ion channel, nuclear receptor, enzyme, member protein - gene list
... Dear All, I want to collect some gene list for GPCR, ion channel, nuclear receptor, enzyme, member protein respectively. Is there any easy way to do that? Thanks. ...
member gpcr nuclear enzyme ion written 5 weeks ago by Shicheng Guo8.3k
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Answer: A: R script to download all abstracts of Nature in 2020 from Pubmed
... Find another way as good as @Alex Nesmelov's proposal. Thanks Alex Nesmelov! library(easyPubMed) my_query <- 'Damiano Fantini[AU] AND "2018"[PDAT]' my_entrez_id <- get_pubmed_ids(my_query) my_abstracts_txt <- fetch_pubmed_data(my_entrez_id, format = "abstract") ...
written 5 weeks ago by Shicheng Guo8.3k

Latest awards to Shicheng Guo

Popular Question 1 day ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Scholar 7 weeks ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
Popular Question 9 weeks ago, created a question with more than 1,000 views. For LD plot for both microsatellites and SNP data (Haploview)
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: What is a typical workflow to correlate methylation and expression data?
Great Question 12 weeks ago, created a question with more than 5,000 views. For trim_galore and cutadapt to paired-end DNA sequencing
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Great Question 3 months ago, created a question with more than 5,000 views. For trim_galore and cutadapt to paired-end DNA sequencing
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
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 LD plot for both microsatellites and SNP data (Haploview)
Student 4 months ago, asked a question with at least 3 up-votes. For Converting Phred64 fastq to Phred33 fastq
Popular Question 4 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Area under the ROC Curve for genetic data
Popular Question 4 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Great Question 5 months ago, created a question with more than 5,000 views. For fastq-dump split-spot and skip-technical
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Popular Question 5 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 5 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10

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