Moderator: Vincent J. Carey, Jr.

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Posts by Vincent J. Carey, Jr.

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Job: Developer/bioinformatician positions at Harvard Medical School
... Full-time positions are available at Channing Division of Network Medicine, Brigham and Women's Hospital, Boston MA USA. These positions involve work with Bioconductor and various projects in medical genomics. Job descriptions and application instructions are available through the links below: ...
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Comment: C: I am having trouble recreating the linear regression results published in an Alz
... I will not be looking at synapse, so cannot help with that. You might want to work from the GEO deposit, checking that it is consistent with the synapse content. If the datasets are consistent, you would be able to post a fully reproducible example based on the GEO data and then you might get more ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: I am having trouble recreating the linear regression results published in an Alz
... 1) Did you contact the authors? They should provide code that you could study/use/improve. 2) You do not describe how you retrieve the data to run your script. Your script is long and hard to digest. I used GEOquery to obtain some of the data from GEO, and was able to do a sanity check of the as ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How to reconfigure Jupyter Notebook to locate specific version of R?
... I have confirmed that this strategy works. You have to find the right kernel.json and ensure that the version of R you want to use has a functioning IRkernel package installed. ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How to reconfigure Jupyter Notebook to locate specific version of R?
... Can I suggest that you use jupyter --data-dir to find the folder where ir/kernel.json lives In that json file there is an object that looks something like this {"argv": ["R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"], "display_name":"R", "language":"R" ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Sorry to lose the thread here. If the problem persists we could try a google hangout before 1pm ET today. ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... This message on the C compiler is news to me. Do you have xcode developer tools installed? Or gcc installed via anaconda, or homebrew? See http://r.research.att.com/tools/ for much relevant information. ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Maybe this afternoon we can do a screenshare. I will be out for a couple of hours. Jupyter is just gobbling up the key information, you need to work outside of it and all will be well eventually. I don't think too many people administer R through jupyter ... once it is properly set up Jupyter is ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Are you sure all the 00LOCK* files are removed? We need a log. Can you run R in Terminal, issue BiocManager::install("BiocParallel") and capture and post the resulting textual messages which should include the failure? Command-A to select, Command-C to copy, Command-V to paste into the support si ...
written 9 months ago by Vincent J. Carey, Jr.6.3k
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... We need a log. Where are you located? Would you want to do a google hangout to try to dig into your configuration? ...
written 9 months ago by Vincent J. Carey, Jr.6.3k

Latest awards to Vincent J. Carey, Jr.

Popular Question 11 months ago, created a question with more than 1,000 views. For edX online course introducing Bioconductor now up and running
Supporter 11 months ago, voted at least 25 times.
Appreciated 2.5 years ago, created a post with more than 5 votes. For edX online course introducing Bioconductor now up and running
Scholar 3.6 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Scholar 3.8 years ago, created an answer that has been accepted. For A: How to get list of E.coli genes wit their details on Genome?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For C: how can I install packages in docker/R/bioconductor so that they persist?
Centurion 5.3 years ago, created 100 posts.

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