User: shoujun.gu

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shoujun.gu340
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340
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Rockville/MD
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2 months, 2 weeks ago
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1 year, 7 months ago
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Posts by shoujun.gu

<prev • 72 results • page 1 of 8 • next >
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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 3 months ago by shoujun.gu340
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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 5 months ago by shoujun.gu340
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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 5 months ago by shoujun.gu340
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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 5 months ago by shoujun.gu340
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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 5 months ago by shoujun.gu340
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Comment: C: Cannot install NumPy using pip and import it
... Did you start the virtual environment first? ...
written 6 months ago by shoujun.gu340
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Answer: A: I don't know how to make this bioinformatic picture
... Its a typical genome browser visualization. You can get this kind of visualization in any genome browser. Under the hood, it’s just a histogram. If you have the data, you can make these plots by any data visualization tools, there are various modules in python, R or JavaScript. ...
written 6 months ago by shoujun.gu340
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Answer: A: Identify driver mutations instead of genes
... https://www.ncbi.nlm.nih.gov/pubmed/?term=Cell+173%2C+371%E2%80%93385%2C+April+5%2C+2018 ...
written 6 months ago by shoujun.gu340
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Comment: C: TCGA FPKM-UQ method theory
... My understanding is, in statistics view, using 75th percentile read count value to normalize the sample will be less affected by the outliers. ...
written 6 months ago by shoujun.gu340
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Comment: C: Algorithms for finding nearest range given two lists of ranges?
... If you could give some examples, it will help us understand your problems much easier... And in your code, you didn't explain what the 'interval_tree' and 'find_nearest_in_hits' variables are ...
written 6 months ago by shoujun.gu340

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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Remove gap from files
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