User: mforde84

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mforde84940
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Posts by mforde84

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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... my personal favorite is irreparably breaking your xsession, or breaking a mount point so you can't boot past initramfs ...
written 26 days ago by mforde84940
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... using sudo, dd, parted or any combination thereof ... like a moron. ...
written 26 days ago by mforde84940
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... drawingbiological insights into a dataset solely from GO enrichment analysis ...
written 26 days ago by mforde84940
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... Running statistical analyses with no understanding of the tests your using, why you're using them, when it's appropriate to use them, how your data needs to be formated, normalize, or scaled to use them... but hey, you made a volcano plot... so it must be publication quality. right? read the damn pa ...
written 26 days ago by mforde84940
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Comment: C: Which of my mutations are SNPs? Is there an R package to annotate them?
... Any single point mutation is technically a SNP. Well I guess that's not entirely true for a single point indel. But still, any mutation causing a change in a single base to a reference is a SNP. Larger mutations are typically referred to as "structural variants". You can look at something like dbSNP ...
written 26 days ago by mforde84940
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Comment: C: Which of my mutations are SNPs? Is there an R package to annotate them?
... So what type of files do you have? Or could you give a sample format of your data? ...
written 26 days ago by mforde84940
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Comment: C: Resources for gene signature creation
... Great suggestion. I think I'm going to try the lasso regression and see what I pull out. ...
written 27 days ago by mforde84940
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Comment: C: Resources for gene signature creation
... Oh ok, I see. This makes a lot of sense. Unfortunately the number of DEG is high (~2k unique across all three groups). They are tumor samples, so heterogeneity is expected. At the very least it makes sense to go back and double check the #DEG I have is accurate, and contrast the limma results with ...
written 27 days ago by mforde84940
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Comment: C: Professor assign me some tasks, gene ontology sucks. Anyone please guide me, i a
... Given the information you provided, I'm not entirely clear how to help you. I'm not sure how to make gene ontology enrichment analysis suck less for you. ...
written 27 days ago by mforde84940
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Comment: C: Resources for gene signature creation
... Thanks for the suggestions, Kevin. It's a categorical factor. We integrated mRNA and and miRNA data with SNFtool to generate three clusters that show DEG, pathway, and survival differences. However for validation purposes, it's difficult to find independent datasets in the wild which are of our spe ...
written 27 days ago by mforde84940

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Supporter 27 days ago, voted at least 25 times.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Declining quality of biostars
Scholar 9 weeks ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
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Scholar 5 months ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
Scholar 5 months ago, created an answer that has been accepted. For A: SNP analysis based on RNAseq data using GATK PIPELINE
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