User: pacman

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pacman50
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2 months ago
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3 years, 2 months ago
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Posts by pacman

<prev • 6 results • page 1 of 1 • next >
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Is BED file generated by bametobed sorted ?
... We use bamtobed to covert bam files to bed files. I am wondering if the output is sorted by default , because our output bed files seems to be sorted by chromosome and position. I am asking this question because we are using bedtools to calculate coverage with large bam files which takes up a lot ...
bedtools ngs bamtobed coverage sequencing written 11 weeks ago by pacman50 • updated 11 weeks ago by Alex Reynolds26k
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scRNA-seq: how to visualize SNN-Cliq clustering result
... I am comparing various clustering methods for scRNA-seq data. Does it make sense to show SNN-Cliq clustering result on a 2D tSNE plot? I am asking because one of the methods I am testing is kmean clustering of the PCA (which then use tSNE for visualization). A direct comparison between those two me ...
single-cell snn-cliq snn tsne scrnaseq written 16 months ago by pacman50
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How to use SPARQL to query OBO on Protege
... Hello, I have downloaded an ontology for chemical structure in OBO format ( [Classyfire][1]) , but I found it difficult to extract information on Protege by using SPARQL and SNAP-SPARQL. Some Annotations property has rdf and owl classes (e.g rdf:type owl:class), but most of them don't have one. I ...
obo rdf ontology sparql protege written 22 months ago by pacman50
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Comment: C: Batch Download from PubMed ftp server
... yes, it works, but not all PMC articles can be found on FTP server due to copyright issues :(  ...
written 3.2 years ago by pacman50
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Answer: A: Batch Download from PubMed ftp server
... Hi, I found a trick that make the process go a little bit faster.  1.) Find the corresponding PMC ID ( you can find it from PMC-ids.csv.gz)   2.) Follow the format of this URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMCXXXXXX/pdf -> this URL will re-direct the browser to the download link if ...
written 3.2 years ago by pacman50
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Batch Download from PubMed ftp server
... I have a list of articles (couple hundreds) that I would like to download the full text from PubMed central in PDF. Unfortunately, even though all of them can be found at PubMed central ,I can only download less than 10% of them from the FTP service ,based on the file_list.pdf.txt.  I am wondering i ...
ncibi pubmed written 3.2 years ago by pacman50 • updated 3.2 years ago by Danielson30

Latest awards to pacman

Student 16 months ago, asked a question with at least 3 up-votes. For How to use SPARQL to query OBO on Protege
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Batch Download from PubMed ftp server

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