User: Zhilong Jia

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Zhilong Jia1.1k
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a bioinformatician

Posts by Zhilong Jia

<prev • 212 results • page 1 of 22 • next >
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Answer: A: Encode RNA-seq expression matrix
... It seems there are options for hg19 in the File section. See figure https://imgurl.org/temp/1801/80f8198d2a80f2db.png . ...
written 1 day ago by Zhilong Jia1.1k
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Answer: A: Writing PLINK PED and MAP files... Error: Could not open temporary file.
... A related post: https://www.biostars.org/p/46060/ ...
written 11 weeks ago by Zhilong Jia1.1k
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Answer: A: Converting between drug identifier formats
... Convert the PubChem IDs to CHEMBL IDs (In the `Output IDs` section, choose `Registry IDs` - `CHCMBL`.) via https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi ...
written 12 weeks ago by Zhilong Jia1.1k
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Comment: C: what should be taken care of during the bioinformatic analysis for targeted rese
... As @Fabio indicated, "Actually, if possible you should align to the whole genome anyway, so that you avoid spurious alignments to your regions of off-target reads that may have been generated.", in which specific step, the `--intervals` should be used? Thank you. ...
written 4 months ago by Zhilong Jia1.1k
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Comment: C: what should be taken care of during the bioinformatic analysis for targeted rese
... without `--intervals`, what will be different except the time-consumption? Thank you. ...
written 4 months ago by Zhilong Jia1.1k
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Comment: C: Phred score check for BAM files
... The results are not consistent with [determine-phred][1]. I'm not sure which one is correct. if there is '?' or numbers, it should be Q33. With this case, `determine-phred` is right. It seems that the `determine-phred` accepts a revised sam format ( deleting the lines start with @ ). A phred score r ...
written 4 months ago by Zhilong Jia1.1k
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what should be taken care of during the bioinformatic analysis for targeted resequencing, compared with whole genome resequencing?
... what should be taken care of during the bioinformatic analysis pipeline for targeted resequencing, compared with whole genome resequencing? Esp. considering the difference of data between targeted resequencing and whole genome resequencing, What can be done to optimise the bioinformatics pipeline fo ...
wgs targeted resequencing sequencing written 4 months ago by Zhilong Jia1.1k • updated 4 months ago by finswimmer660
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Comment: C: can picard use multiple threads?
... It seems the Elapsed times have no difference. ...
written 6 months ago by Zhilong Jia1.1k
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Comment: C: To get genes for each clusters from heatmap
... use `hclust` function with "euclidean" distance by default. you can find the pattern in the screenshot with the code. require(graphics) hc <- hclust(dist(USArrests), "ave") hc$order hc$labels plot(hc) ![enter image description here][1] ![enter image description here][2] ...
written 6 months ago by Zhilong Jia1.1k
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Comment: C: Ensembl Ids To Gene Name Conversion
... Just update the [ensembl][1] url. [1]: http://www.ensembl.org/biomart/martview/8a62d485840abc94bd821e620e18a1c7 ...
written 7 months ago by Zhilong Jia1.1k

Latest awards to Zhilong Jia

Popular Question 13 days ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Student 9 weeks ago, asked a question with at least 3 up-votes. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How can we make this plot? (sequence logo)
Popular Question 3 months ago, created a question with more than 1,000 views. For How to calculate connectivity score for a compound in connectivity map O2?
Popular Question 4 months ago, created a question with more than 1,000 views. For A list of Bioinformatics projects for volunteers
Popular Question 4 months ago, created a question with more than 1,000 views. For How to calculate connectivity score for a compound in connectivity map O2?
Popular Question 6 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question 7 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question 8 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Epic Question 8 months ago, created a question with more than 10,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Popular Question 11 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Great Question 16 months ago, created a question with more than 5,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 17 months ago, created a question with more than 1,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 17 months ago, created a question with more than 1,000 views. For Database for Chemical and Physical Properties of drugs or compounds
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Generate Bed File Only Containing The Cds Region ?
Popular Question 19 months ago, created a question with more than 1,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 19 months ago, created a question with more than 1,000 views. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Prophet 19 months ago, created a post with more than 20 followers. For A list of Bioinformatics projects for volunteers
Guru 19 months ago, received more than 100 upvotes.
Scholar 22 months ago, created an answer that has been accepted. For A: Batch effect removal before merging microarray data sets
Appreciated 23 months ago, created a post with more than 5 votes. For A list of Bioinformatics projects for volunteers
Scholar 23 months ago, created an answer that has been accepted. For A: Batch effect removal before merging microarray data sets
Popular Question 23 months ago, created a question with more than 1,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 23 months ago, created a question with more than 1,000 views. For how to plot multi pheatmap into one figure

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