User: Michele Busby

gravatar for Michele Busby
Michele Busby2.0k
Reputation:
2,020
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Location:
United States
Website:
http://scotty.genetics...
Twitter:
michelebusby
Last seen:
1 week, 1 day ago
Joined:
6 years, 5 months ago
Email:
b************@gmail.com

Computational biologist at an oncology startup, formerly at the Broad Institute. I developed Scotty application for performing RNA Seq power analysis while completing my PhD in Gabor Marth's lab.

Posts by Michele Busby

<prev • 132 results • page 1 of 14 • next >
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Comment: C: Free for academic use only licenses (If you want to sell your software please ju
... I have honestly never gotten all the way through the process of purchasing academic software because of the problems above. I would expect the software to be documented and tested and not really require support. But that is what I expect of open source software and it is largely the case. (Now, thi ...
written 10 weeks ago by Michele Busby2.0k
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Blog: Free for academic use only licenses (If you want to sell your software please just sell your software)
... As a bioinformatician in industry, if you are and academic who wants to charge for your software, please don’t do this: Software is free for academic use only. For industry use, please contact our lawyers. Please do this: For industry use, software costs $[price] per license. Click here to downlo ...
blog licensing written 10 weeks ago by Michele Busby2.0k • updated 10 weeks ago by Chris Miller21k
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Comment: C: Detecting highly variable genes within replicates
... I don't think you need to assume a normal distribution but I haven't looked at the theory in a while. The main thing is that you can add uncorrelated variances to get the total variance. They are probably something like a lognormal distribution but the tail is constrained by biology so you can usual ...
written 4 months ago by Michele Busby2.0k
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Answer: A: Detecting highly variable genes within replicates
... This is a good question and you were wise to ask it because I don't think the obvious approach is the correct one. For RNA Seq, the observed variance that you get from calculating the variance in the replicates will have a mixture of biological + technical variance. If the libraries are good, the ...
written 4 months ago by Michele Busby2.0k
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Answer: A: HLA Typing understanding
... I am not sure at what level you are confused, so forgive me if this is too basic. This is an explainer on how the HLAs are named: http://hla.alleles.org/nomenclature/naming.html Functionally, you only care about the first few digits. HLA-A - this is the gene. There are a bunch of HLA genes. HL ...
written 10 months ago by Michele Busby2.0k
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Comment: C: DNA Hybridization Melting Temperature Open Source
... Thank you Pierre! That did the trick ...
written 12 months ago by Michele Busby2.0k
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DNA Hybridization Melting Temperature Open Source
... Hi, Is there a good open source software for calculating the melting temperature of two DNA sequences? I have been trying the Biopython MeltingTemp module but it relies on tables for the possible mismatches and many of the possible mismatches are not in the tables, so my sequences get kicked out. ...
sequence written 12 months ago by Michele Busby2.0k • updated 12 months ago by Pierre Lindenbaum121k
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Answer: A: Statistical test for replicates
... When you sequence small RNA you often get reads that are the degradation products of longer mRNA. These might be what you are seeing. It will be better or worse depending on the protocol. If it is just a size selection there will be a lot of junk. If you are looking for miRNA there is an enzyme that ...
written 12 months ago by Michele Busby2.0k
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Answer: A: fastq- dump error
... I got this today too and it actually proceeded through to the whole download even though it had the error message. So maybe wait and see if it finishes? You can do an "ls" to see if it's still loading. If it gives you the stats at the end it's good. ...
written 12 months ago by Michele Busby2.0k
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Answer: A: RSEM build for C. elegans
... I figured it out but I'll leave it here if anyone else runs into this: RSEM expects a ; after the transcript_id. It's not here in this version of the file. This adds the : to the line and seems to fix it: sed -i 's/$/;/' c_elegans.PRJNA13758.WS253.canonical_geneset.fixed.gtf ...
written 13 months ago by Michele Busby2.0k

Latest awards to Michele Busby

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Chip-Seq merging peak files
Appreciated 12 months ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Appreciated 12 months ago, created a post with more than 5 votes. For A: Chip-Seq merging peak files
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 17 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Scholar 17 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Popular Question 22 months ago, created a question with more than 1,000 views. For Tool For Visualizing Sections Of Sequences
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
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Scholar 2.6 years ago, created an answer that has been accepted. For A: Coverage for sample with many species
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 3.5 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
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Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species

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