User: Alejandro Reyes

gravatar for Alejandro Reyes
Alejandro Reyes1.6k
Reputation:
1,610
Status:
Trusted
Location:
Dana-Farber Cancer Institute, Boston, USA
Twitter:
@areyesq
Scholar ID:
Google Scholar Page
Last seen:
14 hours ago
Joined:
6 years, 11 months ago
Email:
a*****************@gmail.com

Posts by Alejandro Reyes

<prev • 279 results • page 1 of 28 • next >
0
votes
0
answers
64
views
0
answers
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 4 days ago by Alejandro Reyes1.6k
0
votes
0
answers
51
views
0
answers
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 8 days ago by Alejandro Reyes1.6k
0
votes
0
answers
58
views
0
answers
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 13 days ago by Alejandro Reyes1.6k
0
votes
0
answers
58
views
0
answers
Comment: C: DEXSeq 1.26.0 running very slowly (stuck?)
... Hi Lance. Do you know at which step it is getting stuck?  ...
written 5 weeks ago by Alejandro Reyes1.6k
0
votes
1
answer
149
views
1
answers
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 7 weeks ago by Alejandro Reyes1.6k
0
votes
1
answer
149
views
1
answers
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 9 weeks ago by Alejandro Reyes1.6k
2
votes
1
answer
170
views
1
answers
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 3 months ago by Alejandro Reyes1.6k
2
votes
2
answers
129
views
2
answers
Answer: A: DEXSeq and DRIMSeq on paired samples?
... Hi zoe.ward,  For DEXSeq's vignette, this is documented in the section "4 Additional technical or experimental variables". Please let us know if something is not clear. Shortly, you need to pass the following formulae to both estimateDispersions and testForDEU: formulaFullModel = ~ sample + exon + ...
written 4 months ago by Alejandro Reyes1.6k
0
votes
1
answer
138
views
1
answers
Answer: A: Dexseq output interpretation
... Hi yelekley, I think the answers to these questions are in the section "2.4 Preparing the annotation" of the DEXSeq vignette. Did you already have a look at it? If something is unclear from this description please let us know and we will be happy to clarify it.  ...
written 5 months ago by Alejandro Reyes1.6k
2
votes
0
answers
156
views
0
answers
Comment: C: DEXSeq analysis with large number of samples
... Yeah, the GLMs can take very long to fit when the models are large. One option is just to configure a BPPARAM with a cluster configuration and distribute it across many jobs. With such number of samples some of the steps from DEXSeq might not be needed. I would have a look at the diffSplice function ...
written 6 months ago by Alejandro Reyes1.6k

Latest awards to Alejandro Reyes

Scholar 19 months ago, created an answer that has been accepted. For A: DEXSeqHTML and biomart object
Scholar 19 months ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Translating model formula from DESeq to DEXSeq
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: DEXSeq with mutliple experimental conditions - definig contrasts
Scholar 2.8 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.0 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Scholar 3.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: DEXSeq and Independent filtering
Scholar 3.2 years ago, created an answer that has been accepted. For A: Translating model formula from DESeq to DEXSeq
Centurion 4.0 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 318 users visited in the last hour