User: shoujun.gu

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shoujun.gu370
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Rockville/MD
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1 year, 2 months ago
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Posts by shoujun.gu

<prev • 76 results • page 1 of 8 • next >
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Comment: C: Creation of a VCF file from scratch with python
... you can do it easily in pandas package. ...
written 15 months ago by shoujun.gu370
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Comment: C: Why MAF file number not match with case number in firebrowse?
... Thank you for your reply! The reason I looked for the data in Firebrowse is because they provided the normalized RNASeq data between cases, where GDC data portal do not have (correct me if I'm wrong). ...
written 15 months ago by shoujun.gu370
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Comment: C: Why MAF file number not match with case number in firebrowse?
... The Annotation mutation file I download is: Mutation_Packager_Calls (MD5) with file name: gdac.broadinstitute.org_COAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz The Raw Annotation mutation file I download is: Mutation_Packager_Raw_Calls (MD5) with file name: gdac.broadinstitute.org_ ...
written 15 months ago by shoujun.gu370
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Why MAF file number not match with case number in firebrowse?
... I found there are 460 cases in COAD from Firebrowse. But in the downloaded Mutation Annotation files, there are only 154 MAF files. I'd like to know why there is significantly less MAF files than case number? And in the downloaded Raw Mutation Annotation files, there are 367 MAF files (still less ...
genome next-gen snp written 15 months ago by shoujun.gu370 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: sed regex code help wanted
... I found the strings you want all contains single underscore in it, while the ones you don't want all contains double underscores in it...Thus it is pretty easy to separate them, do not even need to use regex. But I'm not good at sed, I don't know how to do it in sed. but, in python, you can split ...
written 21 months ago by shoujun.gu370
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Comment: C: Help understand RNAseq deconvolution results?
... You may get some idea from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906687/ ...
written 2.0 years ago by shoujun.gu370
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Comment: C: Help understand RNAseq deconvolution results?
... Since I'm not in this field, could you explain what that corr fig means? why all diagonal are 1? eg, the first block (adipocyte, ctrl1) value =1, which indicates adipocyte are perfect corr with ctrl1. What's this mean? ...
written 2.0 years ago by shoujun.gu370
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Comment: C: Get the GO terms associated to all genes contained in a list with Python
... If you can find the file with gene names and the terms you need. (maybe some file in http://www.geneontology.org/) Then it's just the dataframe processing job.. ...
written 2.0 years ago by shoujun.gu370
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Comment: C: Help understand RNAseq deconvolution results?
... Deconvolution algorithm is used to estimate the relative abundance of a cell type in the sample. Thus, it's always >=0. You should always label your color bar, so that people can understand the result. Fig2 maybe the plot of the raw data from RNAseq deconvolution results. But Fig1, the data mus ...
written 2.0 years ago by shoujun.gu370
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Comment: C: Cannot install NumPy using pip and import it
... Did you start the virtual environment first? ...
written 2.1 years ago by shoujun.gu370

Latest awards to shoujun.gu

Appreciated 21 months ago, created a post with more than 5 votes. For A: How to manipulate a gff or gtf file manually?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 2.7 years ago, created an answer that has been accepted. For A: Kallisto run error
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Scholar 2.7 years ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 2.7 years ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 2.7 years ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 2.8 years ago, created an answer that has been accepted. For A: Kallisto run error

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