User: shoujun.gu

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shoujun.gu330
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330
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Location:
Rockville/MD
Last seen:
3 days, 2 hours ago
Joined:
1 year, 1 month ago
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Posts by shoujun.gu

<prev • 67 results • page 1 of 7 • next >
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Comment: C: Cannot install NumPy using pip and import it
... Did you start the virtual environment first? ...
written 8 days ago by shoujun.gu330
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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 8 days ago by shoujun.gu330
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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 9 days ago by shoujun.gu330
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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 9 days ago by shoujun.gu330
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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 9 days ago by shoujun.gu330
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Comment: C: TCGA BRCA Solid Tissue Normal Filter
... 1. add your files to your cart 2. go to your cart page, there is a 'sample sheet' download button. download that tsv file 3. the sample sheet tsv file contains columns: File ID File Name Data Category Data Type Project ID Case ID Sample ID Sample Type 4. match your sample file name with the 'Samp ...
written 9 days ago by shoujun.gu330
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Answer: A: TCGA BRCA Solid Tissue Normal Filter
... GDC provides the sample sheet file, in which there is the information about whether an sample is normal or tumor. You could filter the samples by writing a python or R script. ...
written 9 days ago by shoujun.gu330
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Answer: A: Pandas and dataframe (filtering)
... 1. add a new column in the dataframe 2. for each row, the value in the new column is the set contains values of qseqid and sseqid. for example, the value of the new column in the first row is {seq1_0035_0035, seq13_0042_0035}. 3. drop duplicates using subset: cluster & new column 4. remove t ...
written 12 days ago by shoujun.gu330
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How could I get the normal (control) RNASeq/miRNASeq data from TCGA?
... TCGA let me download the RNASeq/miRNASeq FPKM count data in each patient case. such as: c2357737-ad60-4603-9ce3-4b30cc45d30b.FPKM.txt.gz I'd like to know where can I the the control data? Thanks in advance. ...
rna-seq written 7 weeks ago by shoujun.gu330
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Answer: A: Comparing 2 Columns at once
... here is the python code, replace the real file name in the first two lines: input_file='your_input_file' output_file='your_output_file' import pandas as pd df=pd.read_csv(input_file, index_col=0) col=df.columns col_t=col[:-1] new_col=[col_t[i]+str(i+2) for ...
written 3 months ago by shoujun.gu330

Latest awards to shoujun.gu

Scholar 3 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 8 months ago, created an answer that has been accepted. For A: Kallisto run error
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Scholar 8 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 8 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 8 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 9 months ago, created an answer that has been accepted. For A: Kallisto run error

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