User: Chun-Jie Liu
Chun-Jie Liu • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- US, Houston
- Website:
- https://chunjie-sam-li...
- Twitter:
- chunjie_sam_liu
- Last seen:
- 22 hours ago
- Joined:
- 10 months, 3 weeks ago
- Email:
- c**************@gmail.com
Posts by Chun-Jie Liu
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... Please try python3. And add `requests` module.
Or you can use [R version](https://www.biostars.org/p/233645/#233708) ...
written 10 weeks ago by
Chun-Jie Liu • 230
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... Thanks for your information. ...
written 7 months ago by
Chun-Jie Liu • 230
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...
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 7 months ago by
Chun-Jie Liu • 230
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... 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 7 months ago by
Chun-Jie Liu • 230
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... Thanks for your information. I even miss such good tool before. ...
written 7 months ago by
Chun-Jie Liu • 230
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... 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 7 months ago by
Chun-Jie Liu • 230
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... 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 8 months ago by
Chun-Jie Liu • 230
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... Even though you set running environment well, you really want to use samtools or GATK to call big bam data on your Windows? ...
written 8 months ago by
Chun-Jie Liu • 230
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... 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 8 months ago by
Chun-Jie Liu • 230
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... 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 8 months ago by
Chun-Jie Liu • 230
Latest awards to Chun-Jie Liu
Supporter
3 months ago,
voted at least 25 times.
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
7 months ago,
created an answer that has been accepted.
For A: Obtain Ensembl transcript ids that contain retained introns
Scholar
8 months ago,
created an answer that has been accepted.
For A: Obtain Ensembl transcript ids that contain retained introns
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Extract surrounding genome sequences given certain locations using R
Scholar
8 months ago,
created an answer that has been accepted.
For A: Obtain Ensembl transcript ids that contain retained introns
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