User: Zhenyu Zhang

gravatar for Zhenyu Zhang
Zhenyu Zhang260
Reputation:
260
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Trusted
Location:
United States
Last seen:
1 week, 6 days ago
Joined:
5 years, 9 months ago
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about me

Posts by Zhenyu Zhang

<prev • 61 results • page 1 of 7 • next >
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Need recommendations of RNA-Seq somatic variant calling pipeline
... I am looking for a somatic RNA-Seq variant calling pipeline, that can take tumor RNA-Seq without normals for variant calling. We want production pipelines, that means a stable tool instead of a graduate student project no one used after publication. Currently I have in mind is the GTAK practice, ...
somatic variant rna-seq written 14 days ago by Zhenyu Zhang260
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Comment: C: Are there any GenomeStudio alternatives to process Illumina genotyping array?
... It seems some basics can be done with GS command lines, but still in windows. ...
written 8 weeks ago by Zhenyu Zhang260
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Any adaptive permutation R packages?
... I know there are some standalone tools in the GWAS/eQTL domain using adaptive permutations. Do we have an R package that supports more general usage of permutations? ...
permutation R adaptive permutation written 10 weeks ago by Zhenyu Zhang260
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Comment: A: how to extract unique and the first shared exon in a given gene?
... No code, just general suggestions if I am coding in R - To find the first/last, etc, it's the easiest to sort/order the data.frame/ data.table by several columns and remove duplicates - To find if something is unique or not, it's the easiest to use dplyr group_by() %>% count/summarise - For ...
written 12 weeks ago by Zhenyu Zhang260
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Are there any GenomeStudio alternatives to process Illumina genotyping array?
... The mouse clicking interface of GenomeStudio is so unfriendly for large and continuous data production. - Do we have alternatives to this that can process Illumina genotyping array idat files? - Or do you have any suggestions to automate the GenomeStudio process with command lines? Thanks ...
illumina genotyping array genomestudio written 12 weeks ago by Zhenyu Zhang260 • updated 5 weeks ago by steffanchristiansen0
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Answer: A: Is TCGA PRAD RNA-seq data strand specific?
... The short answer is no. The specific RNA-Seq library preparation kit TCGA used actually "could" support stranded library; however, it was used in a manner that libraries are actually strandless. ...
written 8 months ago by Zhenyu Zhang260
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Comment: C: Why is TCGA Genomic Data Commons missing some data?
... Btw, if you were in the loop during the old TCGA DCC era, there was an emergency redaction of TCGA LAML data for a couple of months. GDC happened to pull TCGA data from DCC and CGHub during that period of time, so that's why they are missing ...
written 9 months ago by Zhenyu Zhang260
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Comment: C: TCGA COAD and READ annotations missing from GDC commons?
... Such annotation still exist in GDC as "annotation" nodes in the GDC Database, and queryable using APIs. As all metadata in GDC are maintained in a single Graph Database and accessible by API (and UI), there are no separate "annotation database" or "annotation manager" in GDC. ...
written 9 months ago by Zhenyu Zhang260
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Comment: C: How to find On-Target and Off-Targer percentage of reads?
... We used HSmetics too. But some large WXS files have extreme memory requirement. Sometimes we have to double memory allocation from 16G to 32G, or even 64G to get this done. We don't see similar problems with WGSmetrics no matter how big the file is. Does anyone know alternatives of HSmetrics? ...
written 15 months ago by Zhenyu Zhang260
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Answer: A: WGS for TCGA HNSC project
... I don't know why the sequencesource will state otherwise, but if there is sdrf describing this vcf is derived from a WGS CGHub analysis_id/bam file, then it should be WGS. As to MAFs, ppl will not make project-level MAFs out of WGS calls given the file will be 100 times larger. ...
written 2.1 years ago by Zhenyu Zhang260

Latest awards to Zhenyu Zhang

Popular Question 5 months ago, created a question with more than 1,000 views. For LiftOver with zero-based UCSC chain file
Popular Question 6 months ago, created a question with more than 1,000 views. For Impute2 race specific panel?
Popular Question 14 months ago, created a question with more than 1,000 views. For Impute2 race specific panel?
Popular Question 22 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 22 months ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Popular Question 22 months ago, created a question with more than 1,000 views. For Tag Snp, Independent Gwas, Eqtl Results
Popular Question 22 months ago, created a question with more than 1,000 views. For tumor only variant calling tools
Popular Question 22 months ago, created a question with more than 1,000 views. For Tcga Gene Id Conversion To Ensembl Or Hgnc
Popular Question 22 months ago, created a question with more than 1,000 views. For gene set enrichment / GO
Popular Question 23 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 24 months ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Popular Question 2.5 years ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Survival Analysis Using Tcga Data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 2.8 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 2.9 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 2.9 years ago, created a question with more than 1,000 views. For MACH imputation result QC
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Eqtl Results Adjusted For Genomic Inflation Factor
Popular Question 3.0 years ago, created a question with more than 1,000 views. For MACH imputation result QC
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Survival Analysis Using Tcga Data
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Survival Analysis Using Tcga Data
Popular Question 3.5 years ago, created a question with more than 1,000 views. For gene set enrichment / GO

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