Moderator: Giovanni M Dall'Olio

Reputation:
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Location:
London, UK
Website:
http://bioinfoblog.it/
Twitter:
dalloliogm
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Last seen:
an hour ago
Joined:
7 years ago
Email:
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Research Associate at the King's College of London. Interested in human population genetics and cancer.

Posts by Giovanni M Dall'Olio

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Comment: C: Infer publication date by Pubmed ID
... I see! That's too bad, it means I really need to get a table then. ...
written 5 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: Infer publication date by Pubmed ID
... That would be a possibility, but I need to do it basically for all the papers ever published! It would be a bit overkill, specially considering that with a SQL query I could simply calculate the max and min pmid per year. How would you structure such a query with the eutils? ...
written 5 weeks ago by Giovanni M Dall'Olio24k
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Infer publication date by Pubmed ID
... I have a table of several thousands of pubmed ids, and I wonder if there is a smart way to infer the publication date for each of them. My first thought was to search for a table somewhere with a column of the pubmed id together with the publication date. However, since the pubmed ids are associat ...
year pmid pubmed written 5 weeks ago by Giovanni M Dall'Olio24k • updated 9 days ago by krushnach8060
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Comment: C: How to add tophat and bowtie to the path?
... No because the paths in the PATH variable will be duplicated: $HOME/bin:/home/name/bin:/home/name/bin:$PATH ...
written 6 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: How to add tophat and bowtie to the path?
... You should also be able to install bowtie2 (2.2.6-2) and tophat (2.1.0) from the Ubuntu Software Center. ...
written 7 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: How to add tophat and bowtie to the path?
... I think **$home** should really be **/home**. export PATH=$PATH:/home/gjjha/Downloads/softwares/bowtie2-2.2.9/index:/home/gjjha/Downloads/softwares/tophat-2.1.1 Having said that, it would be better not to put random folders in the PATH, as Michael mentioned. ...
written 7 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: Broken vcf header, no column name?
... You need the -h option in tabix, to preserve the headers. ...
written 7 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: Generate random genomic positions with R
... Nice but I don't like the for loop. It would be easy and much more elegant to convert it to a function and apply. ...
written 7 weeks ago by Giovanni M Dall'Olio24k
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Answer: A: Generate random genomic positions with R
... I don't think there is a function for it already, but I suggest you to get chromosome lengths from the TxDb.Hsapiens.UCSC.hg19.knownGene object from Homo.sapiens. > library(Homo.sapiens) > seqlengths(TxDb.Hsapiens.UCSC.hg19.knownGene)[1:24] chr1 chr2 chr3 chr4 ...
written 7 weeks ago by Giovanni M Dall'Olio24k
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Comment: C: usearch version, which one use to get results faster?
... What about running it in parallel? ...
written 7 weeks ago by Giovanni M Dall'Olio24k

Latest awards to Giovanni M Dall'Olio

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Great Question 18 days ago, created a question with more than 5,000 views. For The New Grch38 Human Genome Browser Has Arrived!
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Which Genes Are Contained In The Alternate Reference Loci In Hg38?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Scholar 10 weeks ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Great Question 3 months ago, created a question with more than 5,000 views. For The New Grch38 Human Genome Browser Has Arrived!
Appreciated 3 months ago, created a post with more than 5 votes. For A: The Relationship Between Protein Abundance And Protein Function
Appreciated 3 months ago, created a post with more than 5 votes. For A: The Relationship Between Protein Abundance And Protein Function
Popular Question 3 months ago, created a question with more than 1,000 views. For Which Genes Are Contained In The Alternate Reference Loci In Hg38?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Scholar 5 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Scholar 5 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Unable to install SIFT in Ubuntu
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to convert old entrez id to updated-entrez id in R?
Scholar 6 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Automated Literature Search For List Of Genes
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Computing Number Of Nucleotide And Genes On Each Chromosome
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Scholar 6 months ago, created an answer that has been accepted. For A: How TCGA generanker works ?

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