User: jiwpark00

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jiwpark00200
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Posts by jiwpark00

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Comment: C: meta data analysis for clustering
... Most of the datasets are survival. It's like a suppressor screen - you do a genome-wide RNAi, add a drug (or do the RNAi in the presence of a mutant), and see what survived. When you say: " a common approach would be to reduce data to more comparable summary statistics within each dataset, and the ...
written 21 months ago by jiwpark00200
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meta data analysis for clustering
... I know people do this commonly, but what's the best way to go about when it comes to normalizing multiple different datasets for essentially a "meta-analysis" for clustering purposes? Basically, I want to take several different RNAi screens from different papers, normalize them (since their scoring ...
functional genomics meta-analysis clustering written 22 months ago by jiwpark00200
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Answer: A: The Biostar Handbook. A bioinformatics e-book for beginners.
... Congratulations! I've been using Biostars for past 6+ months so I just bought the book. I'm intermediate-savvy with bioinformatics (I can usually figure out what to do if I search on Biostars or Google but I don't know all the codes off my head) so this book will be great in getting my skills up-to- ...
written 3.0 years ago by jiwpark00200
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how to best analyze multiple microarray for diff expres
... What's the best way to analyze multiple microarray samples at once? And by samples, I mean data sets from multiple sources. Nothing crazy. I want to be able to take couple of cancer samples from different groups and find diff expressed genes across all. ...
microarray written 3.0 years ago by jiwpark00200
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Comment: C: Metabolic gene database: The most-frequently mutated metabolic genes in human ca
... Other people had better answers but this may also be helpful: http://www.hmdb.ca/ This is Human Metabolome Database and I think they have links to some KEGG pathways, some which are relevant for cancers, and you could try to dig up mutations in those pathways. ...
written 3.1 years ago by jiwpark00200
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Comment: C: MD5 Hashing for Many Files
... Thank you everyone! I appreciate the help greatly! ...
written 3.1 years ago by jiwpark00200
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usng biomaRt to get gene homologs
... I have a list of text files that contain list of human gene names. I would like to get a list of their homologs in Drosophila and C. elegans. I'm thinking biomaRt would be the way to go about this but can anyone help me? I've added gene names to transcript IDs before but never figured out how to ad ...
d. melanogaster homologs c. elegans written 3.1 years ago by jiwpark00200
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Comment: C: MD5 Hashing for Many Files
... I apologize for my naiveness but how do I put multiple file directories inside {}? In other words: parallel "md5sum directory1/file1 directory1/file2 " :::* like that? Sorry I'm not familiar with parallel commands. ...
written 3.1 years ago by jiwpark00200
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MD5 Hashing for Many Files
... I was wondering, is there a good way to do MD5 hashing to check many files you download from NCBI (genomes, sequences, etc..)? By "many", I mean that say you want to download 1,000 microarray data - is there a good way to do MD5 hashing to check for identity of the files? I know you can write for ...
md5 rna-seq written 3.2 years ago by jiwpark00200
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Comment: C: Getting RNA-seq Data From ENA (or GEO/SRA)
... I heard of SRAtoolkit. Is it command-line friendly also? I saw in literature people using SRAdb (R) to pull say, platform-specific RNA-seq files. But I'm not sure if that's better than SRAtoolkit or whether SRAdb (or any R package) let you pull RNA-seq file specific to your experiments of interest. ...
written 3.2 years ago by jiwpark00200

Latest awards to jiwpark00

Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: The Biostar Handbook. A bioinformatics e-book for beginners.
Popular Question 21 months ago, created a question with more than 1,000 views. For MD5 Hashing for Many Files
Popular Question 21 months ago, created a question with more than 1,000 views. For Biopython on the web (Flask or Django)
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: The Biostar Handbook. A bioinformatics e-book for beginners.
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: I am really pissed off by the bioinformatics software world. Do/can we have a be

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