User: Zhenyu Zhang

gravatar for Zhenyu Zhang
Zhenyu Zhang270
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270
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Trusted
Location:
United States
Last seen:
4 months, 3 weeks ago
Joined:
6 years, 9 months ago
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Posts by Zhenyu Zhang

<prev • 62 results • page 1 of 7 • next >
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Looking for superfast heatmap algorithm
... We are planing to develop a gene expression heatmap web visualization, so I am looking for a superfast heatmap algorithm for gene expression data. - I don't care about the frontend, b/c we are going to develop our own. We are just looking for algorithm that can cluster genes and patients, and gene ...
heatmap written 5 months ago by Zhenyu Zhang270
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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 12 months ago by Zhenyu Zhang270
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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 14 months ago by Zhenyu Zhang270
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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 14 months ago by Zhenyu Zhang270
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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 15 months ago by Zhenyu Zhang270
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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 15 months ago by Zhenyu Zhang270 • updated 10 months ago by freeseek100
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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 20 months ago by Zhenyu Zhang270
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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 21 months ago by Zhenyu Zhang270
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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 21 months ago by Zhenyu Zhang270
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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 2.3 years ago by Zhenyu Zhang270

Latest awards to Zhenyu Zhang

Popular Question 18 months ago, created a question with more than 1,000 views. For LiftOver with zero-based UCSC chain file
Popular Question 18 months ago, created a question with more than 1,000 views. For Impute2 race specific panel?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Impute2 race specific panel?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 2.9 years ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Tag Snp, Independent Gwas, Eqtl Results
Popular Question 2.9 years ago, created a question with more than 1,000 views. For tumor only variant calling tools
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Tcga Gene Id Conversion To Ensembl Or Hgnc
Popular Question 2.9 years ago, created a question with more than 1,000 views. For gene set enrichment / GO
Popular Question 2.9 years ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 3.0 years ago, created a question with more than 1,000 views. For help: smartpca plot population shift problem
Popular Question 3.1 years ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Popular Question 3.5 years ago, created a question with more than 1,000 views. For CNV calling for illumina 550k array
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Survival Analysis Using Tcga Data
Popular Question 3.6 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 3.8 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 3.9 years ago, created a question with more than 1,000 views. For tools to download multiple files from SRA
Popular Question 3.9 years ago, created a question with more than 1,000 views. For MACH imputation result QC
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Eqtl Results Adjusted For Genomic Inflation Factor
Popular Question 4.0 years ago, created a question with more than 1,000 views. For MACH imputation result QC
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Survival Analysis Using Tcga Data
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Survival Analysis Using Tcga Data
Popular Question 4.5 years ago, created a question with more than 1,000 views. For gene set enrichment / GO

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