Moderator: karl.stamm

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karl.stamm3.4k
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Posts by karl.stamm

<prev • 447 results • page 1 of 45 • next >
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Comment: C: Cluster samples based on expression of a subset of genes
... Take a look at bioconductor/rgsepd where I run DESeq to find genes with differences, then GOSeq to find gene groups of significance, then it moves on to what you're asking for directly. Subset the counts matrix by gene set, PCA on the sub-space, and youll get clustering with respect to named gene se ...
written 20 days ago by karl.stamm3.4k
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Comment: C: Why is 0/0 homozygous reference call in VCF useful information?
... I like to know the difference between "confident data we see hom-ref" and "no-data". Your single-sample VCF is only showing mutant sites, but I often run a VCF at a given set of coordinates, and I want to know which of the four situations is going on. 0/0 or 0/1 or 1/1 or no-data. ...
written 4 weeks ago by karl.stamm3.4k
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Comment: C: Neural networks feature importance
... Sorry I am not familiar with anything called Garson. So it's not clear what you mean by importances. I use least-squares optimization (minimize sum of squared differences) with customized endpoints, sometimes using what TensorFlow calls a softmax activation function. ...
written 8 weeks ago by karl.stamm3.4k
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Comment: C: Neural networks feature importance
... Multiple outcomes are useful if the classification is not binary. Perhaps there are two dimensions being evaluated simultaneously. Multiple classification can use as many outputs as classes in a "one-hot" encoding. If the training algorithm needs a single value for goodness of fit, the multiple o ...
written 9 weeks ago by karl.stamm3.4k
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Answer: A: Neural networks feature importance
... You should be able to use your preferred algorithm to evaluate your network if you customize it to suit the structure. Either the algorithm needs adjustment or the network structure. Typically one output neuron is sufficient to classify something to binary, since it will read 0 or -1 for FALSE, an ...
written 9 weeks ago by karl.stamm3.4k
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Comment: C: Workstation : More RAM or Faster RAM
... If I had enough RAM I would then like faster RAM. ...
written 9 weeks ago by karl.stamm3.4k
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Comment: C: Workstation : More RAM or Faster RAM
... Part of the skill in using cloud services is finding how to reduce the bandwidth required. ...
written 9 weeks ago by karl.stamm3.4k
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Comment: C: What is the fastest protein structure alignment?
... The fastest won't be the most accurate. Define your metrics, how much accuracy is necessary? ...
written 9 weeks ago by karl.stamm3.4k
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Comment: C: How to "simulate" a qPCR reaction in silico?
... It's a complicated problem, and will depend on the environmental context: I'm interested in a tool which can tell me if a qPCR amplification will "go well" when the sample is a blood extraction from Model Organism X. We may have to define "go well" and specify the amplification parameters. ...
written 3 months ago by karl.stamm3.4k
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Comment: C: Methylation analysis request for help
... I searched PLOS One (because their articles are freely downloadable) for 'methylation' and found this article associating methylation patterns to exon usage. Read the methods section carefully and it should help you get a grasp of what to do. https://journals.plos.org/plosone/article?id=10.1371/jo ...
written 3 months ago by karl.stamm3.4k

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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Popular Question 8 months ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 15 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 18 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 22 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 2.7 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 2.7 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
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Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq

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