User: Shixiang

gravatar for Shixiang
Shixiang20
Reputation:
20
Status:
New User
Location:
Shanghai
Website:
http://www.shixiangwan...
Twitter:
ShixiangWang
Last seen:
1 day, 14 hours ago
Joined:
6 months, 3 weeks ago
Email:
s***************@gmail.com

Posts by Shixiang

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Why am I getting different ensembl gene ids for a given gene symbol?
... I got this problem and don't know how to process it. ...
written 14 days ago by Shixiang20
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Comment: C: how to correct gene expression based on tumor purity
... I have same question ...
written 29 days ago by Shixiang20
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Comment: C: Samples with same TCGA barcode in TCGA data
... This function filter barcode following [rules provided by broad institute][1], including Analyte Replicate Filter and Sort Replicate Filter two parts. I update the function to filter samples marked FFPE by broad and test it. The 4th, 5th of `barcode` are FFPE samples. > tcga_replicateFilt ...
written 8 weeks ago by Shixiang20
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Answer: A: How to get the range of LOH?
... You can use `SciClone` without LOH info. Only SNV data is nessary, and it is better to include CNV data. ...
written 8 weeks ago by Shixiang20
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Comment: C: Samples with same TCGA barcode in TCGA data
... Thanks, I wrote a function to solve this. ...
written 8 weeks ago by Shixiang20
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Answer: A: Samples with same TCGA barcode in TCGA data
... Following the rules from broad institute [click][1], I wrote a R function to solve this problem and test it using LUAD tumor barcode. I put it on Github gist [tcga_replicateFilter.R][2] due to word limit on Biostars. This function can help people have related questions. I just check the data @bio ...
written 8 weeks ago by Shixiang20
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Comment: C: Samples with same TCGA barcode in TCGA data
... I download the CNV data by TCGAbiolinks and find no cloumn called `is_ffpe`. Is there a easy way to apply the rules to multiple aliquot ?? ...
written 9 weeks ago by Shixiang20
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Comment: C: Mapping genomic coordinates to protein-relative coordinates
... like [this function][1], but I want to find hg38 other than ensembl version annotation. [1]: https://www.bioconductor.org/packages/3.7/bioc/vignettes/ensembldb/inst/doc/coordinate-mapping.html#3_mapping_genomic_coordinates_to_protein-relative_coordinates ...
written 5 months ago by Shixiang20
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Comment: C: Mapping genomic coordinates to protein-relative coordinates
... The function can translate DNA to Protein sequence, but I am looking for a translation which will think about the location of DNA sequence. ...
written 6 months ago by Shixiang20
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Mapping genomic coordinates to protein-relative coordinates
... How to translate mutations in genome/exome to string of amino acid, with amino acid resulting from the mutation centrally situated. ...
gene R sequence rna-seq snp written 6 months ago by Shixiang20 • updated 6 months ago by arta530

Latest awards to Shixiang

Supporter 4 weeks ago, voted at least 25 times.

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