User: Michele Busby

gravatar for Michele Busby
Michele Busby1.6k
Reputation:
1,650
Status:
Trusted
Location:
United States
Website:
http://scotty.genetics...
Twitter:
michelebusby
Last seen:
6 days, 21 hours ago
Joined:
4 years, 9 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 • 114 results • page 1 of 12 • next >
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Answer: A: RSEM RNAseq - comparison between samples
... If it's RSEM from the archive version of TCGA then there is a field in there which is similar to TPM. See this entry: https://www.biostars.org/p/106127/ If someone ran RSEM more recently and you got that data from them then there is probably something like TPM in there somewhere. Since TPM is no ...
written 23 days ago by Michele Busby1.6k
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Answer: A: Are a Large Number of Biological Replicates Ever an Acceptable Replacement for T
... Yes. Biological replicates will contain both biological variance and technical variance. Therefore, when you run biological replicates you are often "blocking" on both biological noise and technical noise. Since these are usually uncorrelated, the total variance in the system is additive. Where t ...
written 6 weeks ago by Michele Busby1.6k
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Answer: A: Differential expression for two very different samples
... Since the main problem here would be drawing a line through the middle of the genes to normalize the two sets, if you are creating your own data you may want to spike in ERCCs. These are RNA sequences that you would put into each sample in the same quantity to assist with normalization later. In tr ...
written 4 months ago by Michele Busby1.6k
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Comment: C: Retrieving data from new data portal of tcga
... Just in case anyone needs it, here is some example code in Python because JSON is fiddly. If you download the manifest with your FPKM data you can match your files to their info like this: import json fileName='metadata.cart.2017-06-RESTOFID.json' with open(fileName) as data ...
written 4 months ago by Michele Busby1.6k
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Comment: C: IP efficiency in Chip-Seq data
... yeah, what Devon said. ...
written 6 months ago by Michele Busby1.6k
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Answer: A: IP efficiency in Chip-Seq data
... By "fix" do you mean making the less efficient experiment more efficient? The less efficient experiment will have a higher signal to noise ratio, meaning that there will be more background noise. You cannot increase the signal to noise ratio above what is there because you cannot efficiently remove ...
written 6 months ago by Michele Busby1.6k
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Comment: C: Small RNA-seq experimental design, which one is better?
... You could run your experiment with 3-5 reps and then independently validate interesting genes with your remaining replicates. That's a nice experiment. ...
written 7 months ago by Michele Busby1.6k
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Answer: A: Small RNA-seq experimental design, which one is better?
... So with 40 samples you may be able to bring down library prep costs with a high throughput protocol. Usually this means you barcode your individual samples with some sort of in line barcode early on and then you just do one library prep and sequence it. We did this with the RNA Tag Seq protocol for ...
written 7 months ago by Michele Busby1.6k
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Comment: C: Research advice needed
... Hi, try sending me an email and I'll set something up. Thanks, Michele ...
written 9 months ago by Michele Busby1.6k
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Comment: C: Research advice needed
... I can probably only get your started. Are you able to look at things like IGV? ...
written 9 months ago by Michele Busby1.6k

Latest awards to Michele Busby

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Tool For Visualizing Sections Of Sequences
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Appreciated 8 months ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 10 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Centurion 10 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Appreciated 17 months 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 17 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Guru 2.6 years ago, received more than 100 upvotes.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Scholar 3.4 years ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Why Does Rna-Seq Read Count Fit Poisson Distribution?

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