User: Chunjie Liu

gravatar for Chunjie Liu
Chunjie Liu190
Reputation:
190
Status:
Trusted
Location:
US, Houston
Website:
http://chunjie-sam-liu...
Twitter:
chunjie_sam_liu
Last seen:
1 week, 3 days ago
Joined:
6 months, 3 weeks ago
Email:
c**************@gmail.com

Posts by Chunjie Liu

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Protein-protein interactions search (STRING DB)
... Thanks for your information. ...
written 3 months ago by Chunjie Liu190
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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 3 months ago by Chunjie Liu190
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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 3 months ago by Chunjie Liu190
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Comment: C: Identification of SNPs in regulatory regions
... Thanks for your information. I even miss such good tool before. ...
written 3 months ago by Chunjie Liu190
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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 3 months ago by Chunjie Liu190
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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 3 months ago by Chunjie Liu190
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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 4 months ago by Chunjie Liu190
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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 4 months ago by Chunjie Liu190
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Comment: C: Extract surrounding genome sequences given certain locations using R
... Thanks for your correctness. This is a simple example for using biomaRt. The previous version of Ensembl support 'chr' character. You can choose the Ensembl release or genome build by `useMart` or `useEnsembl`. The Ensembl give the [tutorial][1]. [1]: http://useast.ensembl.org/info/data/biomar ...
written 4 months ago by Chunjie Liu190
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Answer: A: Extract surrounding genome sequences given certain locations using R
... You can use [biomaRt][1] GENES = useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "useast.ensembl.org") YouRange<- getBM(attributes = c("chromosome_name", "start_position", "end_position"), filters = c("chromosome_name","start","end"), values = list(chromosome_n ...
written 4 months ago by Chunjie Liu190

Latest awards to Chunjie Liu

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Extract surrounding genome sequences given certain locations using R
Scholar 3 months ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns
Scholar 4 months ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extract surrounding genome sequences given certain locations using R
Scholar 4 months ago, created an answer that has been accepted. For A: Obtain Ensembl transcript ids that contain retained introns

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