User: oganm

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oganm60
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Posts by oganm

<prev • 17 results • page 1 of 2 • next >
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NCBI taxonomy ids in a file
... I am looking for a single file that lists species name for every taxonomy id in NCBI. Is there such a file? I was unable to find a flat file in the taxonomy ftp site. I have been using the site below to manually do the matchings so far but it is quite un-scalable http://www.ncbi.nlm.nih.gov/Taxonom ...
taxonomy written 3.5 years ago by oganm60 • updated 3.5 years ago by genomax67k
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Comparing gene conservation across species
... I have gene lists that I want to compare based on how well they were conserved across human and mice. Is there an established way of doing this? My first impulse was to compare identity directly but since genes have differing lengths and differing functional sizes of differing importance, a measure ...
gene conservation written 4.0 years ago by oganm60 • updated 22 months ago by Biostar ♦♦ 20
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Bright spot on affymetrix chips
... I am doing some quality control on a bunch of affymetrix chip and I noticed a consecutively bright spot in every single one of these chips. I assume this has a technical use since I observed this in different chips. Can anyone tell me what it is? The image below is an example with exceptionally low ...
rna microarray affymetrix written 4.5 years ago by oganm60 • updated 4.5 years ago by Dan D6.8k
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How to get the version history of a bioconductor package
... I wan't to see the version history of an R package in bioconductor but it doesn't seem to exist on package main pages. Does anyone know how can I get that information? It would also be nice to be able to get the previous versions of the package ...
R bioconductor written 4.5 years ago by oganm60 • updated 4.5 years ago by Martin Morgan1.6k
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Comment: C: Finding Gene Symbol Synonyms
... I have an R wrapper for this at https://github.com/oganm/geneSynonym It extracts synonym information about the species of interest and allows you to querry any gene symbol for synonyms. ...
written 4.5 years ago by oganm60
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Comment: C: Missing gene symbols in biomart
... Thanks. In that case do you know what is the data for biomart's ID converter web interface is coming from? ...
written 4.6 years ago by oganm60
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Comment: C: How do you organize your articles?
... Zotero recently released a standalone version that allows integration with other browsers. The only disadvantage is that you need to build it from source which might be troublesome for a windows user. I have no idea how well it stands against other programs but it does have libreoffice integration ...
written 4.6 years ago by oganm60
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Missing gene symbols in biomart
... I have a bunch of swiss prot IDs that I want to convert to hgnc symbols. To do that I am using biomart and for most genes, it works. But for a small minority, it cannot find a corresponding symbol for a given ID even though web interface of biomart successfully handles the conversion. I added an exa ...
R biomart written 4.6 years ago by oganm60 • updated 4.6 years ago by cdsouthan1.8k
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Comment: C: visualizing gene and microarray expression datasets together
... Are you sure about that? Because shRNA's effect can be clearly seen by disappearence of mRNAs. I'd expect miRNAs to act in a comparable manner ...
written 4.8 years ago by oganm60
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Comment: C: Error: could not find function "heatmap.2"
... If you fail to find any function while using R just google it and see which package it comes from. ...
written 4.8 years ago by oganm60

Latest awards to oganm

Popular Question 2.0 years ago, created a question with more than 1,000 views. For NCBI taxonomy ids in a file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to get the version history of a bioconductor package
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to get the version history of a bioconductor package
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Comparing gene conservation across species

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