User: Quak

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Quak270
Reputation:
270
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Location:
United States
Last seen:
11 months, 3 weeks ago
Joined:
4 years, 5 months ago
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a******************@gmail.com

Posts by Quak

<prev • 53 results • page 1 of 6 • next >
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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 11 months ago by Quak270
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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 11 months ago by Quak270
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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 11 months ago by Quak270
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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 12 months ago by Quak270 • updated 12 months ago by Pierre Lindenbaum112k
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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 14 months ago by Quak270
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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 14 months ago by Quak270
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Comment: C: bioinformatics metagenomics analysis towards finding drug candidates
... Thanks for sharing these links and sorry for not making it clear. I am more curious about the computational approaches on this matter rather than experimental efforts. e.g from geneX, in KEGG database, what are the reasonable practices one can take to generate a list of metabolite/protein candidates ...
written 14 months ago by Quak270
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bioinformatics metagenomics analysis towards finding drug candidates
... I wonder what are the possibilities towards finding drug/metabolite candidates using metagenomics data. Metagenomics data only provides prokaryotic related data (well, there would be some host genome as well), I wonder what are the possibility to study host-metagenome interaction towards finding dru ...
metagenomics written 15 months ago by Quak270 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: mapping file for KEGG IDs
... Thanks but I have a KEGG ID list instead of a gene list. ...
written 22 months ago by Quak270
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mapping file for KEGG IDs
... I wonder if there exists any table, mapping kegg entries e.g K01952 to its definition / pathway and modules ? e.g http://www.genome.jp/dbget-bin/www_bget?ko:K01952 ...
kegg written 22 months ago by Quak270 • updated 22 months ago by 5heikki7.7k

Latest awards to Quak

Popular Question 14 months ago, created a question with more than 1,000 views. For generating random newick tree
Popular Question 14 months ago, created a question with more than 1,000 views. For extracting certain region 16sRNA from Silva
Appreciated 21 months ago, created a post with more than 5 votes. For VCF files: Change Chromosome Notation
Popular Question 21 months ago, created a question with more than 1,000 views. For extracting certain region 16sRNA from Silva
Student 21 months ago, asked a question with at least 3 up-votes. For extracting certain region 16sRNA from Silva
Great Question 22 months ago, created a question with more than 5,000 views. For VCF files: Change Chromosome Notation
Popular Question 22 months ago, created a question with more than 1,000 views. For [W::sam_parse1] urecognized reference name; treated as unmapped
Popular Question 2.3 years ago, created a question with more than 1,000 views. For calculating the total length of cDNA for a given gene
Popular Question 2.3 years ago, created a question with more than 1,000 views. For [W::sam_parse1] urecognized reference name; treated as unmapped
Student 2.3 years ago, asked a question with at least 3 up-votes. For extracting certain region 16sRNA from Silva
Popular Question 3.0 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation
Popular Question 3.1 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation
Popular Question 3.9 years ago, created a question with more than 1,000 views. For VCF files: Change Chromosome Notation
Scholar 4.3 years ago, created an answer that has been accepted. For A: Feature extraction from protein sequences for machine learning classification

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