User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.6k
Reputation:
1,610
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Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
Scholar ID:
Google Scholar Page
Last seen:
1 day, 18 hours ago
Joined:
7 years, 1 month ago
Email:
a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 282 results • page 1 of 29 • next >
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Comment: C: DEXSeq With Reduced Annotations
... I agree. If your filters are independent under the null hypothesis, your analysis should be fine. ...
written 1 day ago by Alejandro Reyes1.6k
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Answer: A: DEXSeq: controlling for cell composition
... This error results when the predictors of a regression are linearly dependent (or in your case, highly correlated). This will be a problem for any regression model. However, the cell-type compositions based on your estimates are almost identical across all samples. My suggestion would be to run the ...
written 7 weeks ago by Alejandro Reyes1.6k
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Answer: A: Can DEXseq be used for splicing QTL analysis?
... In principle, it is possible to encode your genotypes as numeric vectors and run DEXSeq using this vector as your condition. A caveat of this approach is that you would have to run DEXSeq on every locus (or at least every time the levels of your condition change). If you have to many samples, this c ...
written 7 weeks ago by Alejandro Reyes1.6k
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Comment: C: How to get missing columns in DEXSeq analysis (exon usage coefficients)
... Could you send me a small reproducible example code along with a small data example (It could be, for example, the first 100 exons of your object)? Alejandro ...
written 8 weeks ago by Alejandro Reyes1.6k
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Comment: C: Add interaction term between variables to DEXSeq design
... Hi zhenzuo2. Definitely, you can test the hypothesis that you wrote down using exactly the formulae that you mentioned. ...
written 9 weeks ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... Thanks for following this Lance. Do you get this problem in general when you use multiple threads? Or only when you specify multiple threads for DEXSeq? ...
written 9 weeks ago by Alejandro Reyes1.6k
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Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... Hi Lance. Do you know at which step it is getting stuck?  ...
written 3 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeqHTML getListElement GRanges error
... Thanks for looking into this Lance!  Thanks for finding the fix for the python script. Could you submit a pull request with your for to this repo: https://github.com/areyesq89/DEXSeq ?   ...
written 3 months ago by Alejandro Reyes1.6k
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Comment: C: DEXSeqHTML getListElement GRanges error
... Thanks for reporting this! I would need more information to track the source of the error. Could you include the complete code that you are using along with the output of sessionInfo()? ...
written 4 months ago by Alejandro Reyes1.6k
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Answer: A: Kallisto output with DEXSeq
... Hi! I have not personally try something like that, but I know that others have use the kallisto output as input to DEXSeq. See for example these two papers from Mark Robinson's lab: 1. https://f1000research.com/articles/5-1356/v1 2. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-01 ...
written 5 months ago by Alejandro Reyes1.6k

Latest awards to Alejandro Reyes

Scholar 21 months ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 21 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.1 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 3.3 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 4.2 years ago, created 100 posts.

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