User: Chun-Jie Liu

gravatar for Chun-Jie Liu
Chun-Jie Liu260
Reputation:
260
Status:
Trusted
Location:
US, Houston
Website:
https://chunjie-sam-li...
Twitter:
chunjie_sam_liu
Last seen:
2 months ago
Joined:
2 years, 7 months ago
Email:
c**************@gmail.com

Posts by Chun-Jie Liu

<prev • 30 results • page 1 of 3 • next >
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Comment: C: how to correct gene expression based on tumor purity
... But if the the purity value is numeric, how to add it into design formula? To classify samples as low, median and high? Is there a method to adjust the gene expression by tumor purity? ...
written 7 months ago by Chun-Jie Liu260
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Comment: C: TCGA UUIDS to TCGA barcode (SampleID) in R
... Please try python3. And add `requests` module. Or you can use [R version](https://www.biostars.org/p/233645/#233708) ...
written 23 months ago by Chun-Jie Liu260
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Comment: C: Protein-protein interactions search (STRING DB)
... Thanks for your information. ...
written 2.4 years ago by Chun-Jie Liu260
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Answer: A: Protein-protein interactions search (STRING DB)
... The following information is old fashioned as @cdsouthan informing me that [HPRD][2] should not be recommended. The data is not updated since 04-13-10. ----- Original answer If you just want to get all PPI by the experiments, you can download data from [BioGRID][1] and [HPRD][2]. Both databas ...
written 2.4 years ago by Chun-Jie Liu260
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Comment: C: Identification of SNPs in regulatory regions
... As Emily_Ensemb mentioned, we can find the promoter target gene by the position. It's very hard to identify the other regulatory elements targets. The [FANTOM][1] also identified the regulatory regions. It provides [PrESSto][2] to view the regulatory element target and enhancer-promoter associati ...
written 2.4 years ago by Chun-Jie Liu260
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Comment: C: Identification of SNPs in regulatory regions
... Thanks for your information. I even miss such good tool before. ...
written 2.4 years ago by Chun-Jie Liu260
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Answer: A: Identification of SNPs in regulatory regions
... You may check this paper [The Ensembl Regulatory Build][1]. Ensembl call the **regulatory region** based on the Chip-seq and genome-wide and protein-specific measurements of DNA binding, histone modifications from ENCODE or other consortia. Ensembl Regulatory Build contains human and mouse data, ...
written 2.4 years ago by Chun-Jie Liu260
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Answer: A: How to annotate a VCF and convert it to a list of genes (names) with defined m
... The [ANNOVAR][1] has a lot of annotation method. You may check the link. [1]:http://annovar.openbioinformatics.org/en/latest/user-guide/download/ ...
written 2.4 years ago by Chun-Jie Liu260
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Comment: C: How to install SAMTools and Gatk on CygWin and how to call it from Window`s Pyth
... Even though you set running environment well, you really want to use samtools or GATK to call big bam data on your Windows? ...
written 2.4 years ago by Chun-Jie Liu260
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Answer: A: retriving barcodes from TCGA using r
... TCGA provide [API ][1] to get the barcode from UUID. I wrote a [python script][2] to map file UUID barcode. Just input the manifest to the script. Now, then. You want to use r to access GDC API, is the same as python. Use `httr` package in the r to post filters to return your result. A simple exa ...
written 2.4 years ago by Chun-Jie Liu260

Latest awards to Chun-Jie Liu

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Extract surrounding genome sequences given certain locations using R
Supporter 2.0 years ago, voted at least 25 times.
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Extract surrounding genome sequences given certain locations using R
Scholar 2.4 years ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns
Scholar 2.4 years ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Extract surrounding genome sequences given certain locations using R
Scholar 2.5 years ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns

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