User: Quak

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Quak300
Reputation:
300
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Trusted
Location:
United States
Last seen:
1 week, 6 days ago
Joined:
5 years, 5 months ago
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a******************@gmail.com

Posts by Quak

<prev • 57 results • page 1 of 6 • next >
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Comment: C: peptides, molecules and proteins derived from a strain
... What would you use for bacterial genome annotation ? Any existing pipeline ? ...
written 13 days ago by Quak300
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Comment: C: peptides, molecules and proteins derived from a strain
... interesting ! looks like a lot of scraping needed ... ...
written 13 days ago by Quak300
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Comment: C: peptides, molecules and proteins derived from a strain
... I just have the genome sequence from NCBI ...
written 13 days ago by Quak300
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peptides, molecules and proteins derived from a strain
... I have a set of species "Bifidobacterium longum" and "Bifidobacterium breve" and I would like to see - computationally, what are the peptides, bioactive molecules, protein that these strain secrete. I was wondering if there is any tool / pipeline out there or if you can point me to a direction where ...
metagenome written 13 days ago by Quak300
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Comment: C: parse nxml file from pubmed
... thanks so much - I can see that ... can you also add where/how I can learn tweaking the pattern matching - e.g I would like to capture methods which in the original xml looks sec-type="materials|methods">Methods ...
written 23 months ago by Quak300
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Comment: C: parse nxml file from pubmed
... thanks, just to update you, that now works, but doesn't catch anything ... may be I should play with I wish there was a way to parse it into a structure format, and then play with different segments. ...
written 23 months ago by Quak300
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Comment: C: parse nxml file from pubmed
... thanks, If I understand correctly, I made the transform.xls file, and then used it as > cat PMC4729119.nxml | xsltproc --novalid transform.xsl but then I got, transform.xsl:1: namespace error : xmlns:xsl: ' ...
written 23 months ago by Quak300
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parse nxml file from pubmed
... I have downloaded pubmed articles from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/ - the files come in nxml format, and I would like to maneuver on each paper and do some NLP. I already tried two packages, 1) > library(xml2) > tt = read_xml("BMC_Cell_Biol/PMC1079802.nxml") > 2) > pa ...
parsing nxml pubmed written 23 months ago by Quak300 • updated 23 months ago by Pierre Lindenbaum122k
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Answer: A: parsing kegg page
... KEGGREST package is the wrench https://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html ...
written 2.2 years ago by Quak300
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parsing kegg page
... I was wondering how I can parse, a page on kegg like this, given the "fpr:FP2_11210" > http://www.kegg.jp/dbget-bin/www_bget?fpr:FP2_11210 I already looked into two Bioconductor packages "pathway" and "Kegg Graph" but didn't find something relevant. I was hoping somebody already might have some ...
kegg written 2.2 years ago by Quak300

Latest awards to Quak

Great Question 23 months ago, created a question with more than 5,000 views. For VCF files: Change Chromosome Notation
Prophet 23 months ago, created a post with more than 20 followers. For VCF files: Change Chromosome Notation
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For VCF files: Change Chromosome Notation
Epic Question 23 months ago, created a question with more than 10,000 views. For VCF files: Change Chromosome Notation
Popular Question 23 months ago, created a question with more than 1,000 views. For global alignment using needleall
Popular Question 23 months ago, created a question with more than 1,000 views. For extracting certain region 16sRNA from Silva
Popular Question 23 months ago, created a question with more than 1,000 views. For pooling 16sRNA samples in UPARSE pipeline
Popular Question 23 months ago, created a question with more than 1,000 views. For What is the easiest way to see the overlap of pair end sequencing data
Popular Question 23 months ago, created a question with more than 1,000 views. For generating random newick tree
Popular Question 23 months ago, created a question with more than 1,000 views. For parse nxml file from pubmed
Popular Question 23 months ago, created a question with more than 1,000 views. For mapping metagenomics samples to multiple references genome
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Feature extraction from protein sequences for machine learning classification
Popular Question 2.1 years ago, created a question with more than 1,000 views. For generating random newick tree
Popular Question 2.1 years ago, created a question with more than 1,000 views. For extracting certain region 16sRNA from Silva
Appreciated 2.7 years ago, created a post with more than 5 votes. For VCF files: Change Chromosome Notation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For extracting certain region 16sRNA from Silva
Student 2.7 years ago, asked a question with at least 3 up-votes. For extracting certain region 16sRNA from Silva
Great Question 2.8 years ago, created a question with more than 5,000 views. For VCF files: Change Chromosome Notation
Popular Question 2.8 years ago, created a question with more than 1,000 views. For [W::sam_parse1] urecognized reference name; treated as unmapped
Popular Question 3.2 years ago, created a question with more than 1,000 views. For calculating the total length of cDNA for a given gene
Popular Question 3.2 years ago, created a question with more than 1,000 views. For [W::sam_parse1] urecognized reference name; treated as unmapped
Student 3.2 years ago, asked a question with at least 3 up-votes. For extracting certain region 16sRNA from Silva
Popular Question 3.9 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation
Popular Question 4.0 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation
Popular Question 4.8 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation

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