User: Brian Haas

gravatar for Brian Haas
Brian Haas90
Reputation:
90
Status:
Trusted
Location:
Last seen:
8 months, 1 week ago
Joined:
4 years, 12 months ago
Email:
b****@broadinstitute.org

Posts by Brian Haas

<prev • 6 results • page 1 of 1 • next >
1
vote
2
answers
169
views
2
answers
Answer: A: Splatter: simulating fold changes for specific genes?
... Thanks, Luke!   I've been going through the splatter code and exploring my options here.  The coding and documentation in splatter is absolutely spectacular!  and that's been a huge help.   I'll be in touch with questions. ...
written 8 months ago by Brian Haas90
4
votes
2
answers
169
views
2
answers
Splatter: simulating fold changes for specific genes?
... Hi - I have an existing set of single cell data that I can use to have Splatter learn the initial set of parameters.  Then, I'd like to adjust the relative gene expression of specific genes so that they'll be simulated at specific higher or lower target levels.  Is there a straightforward way to do ...
splatter written 8 months ago by Brian Haas90
0
votes
2
answers
918
views
2
answers
Answer: A: RNA-Seq, generate batch-free count matrix
... Hi Steve, I think that's right. I put an example of what I was experimenting with here: https://github.com/brianjohnhaas/singleCellRNASeq note, it turned out that I really shouldn't have been trying to remove the 'batch' effect here, because my two plates of cells turned out to be quite differe ...
written 5.0 years ago by Brian Haas90
0
votes
5
answers
7.8k
views
5
answers
Comment: C: RNA-Seq, generate batch-free count matrix
... Many thanks, everyone! I'll see how far I can get with exploring these various methods and I'll post a summary. -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas [[alternative HTML version deleted]] ...
written 5.0 years ago by Brian Haas90
0
votes
5
answers
7.8k
views
5
answers
Comment: C: RNA-Seq, generate batch-free count matrix
... Thanks, Gordon! If I want to also remove effects related to total read counts or coverage biases or other library quality metrics, which sometimes end up being highly correlated with principal component 1, do I include these continuous values as covariates in the removeBatchEffect() method? I was l ...
written 5.0 years ago by Brian Haas90 • updated 4.7 years ago by Gordon Smyth37k
13
votes
5
answers
7.8k
views
10 follow
5
answers
RNA-Seq, generate batch-free count matrix
... Greetings all, I've been researching ways to remove batch effects from RNA-Seq count matrices. Basically, I'm starting with a counts matrix that includes batch effects, and want to generate a new matrix of counts that has the batch effects removed. I'm looking to apply this to sets of RNA-Seq samp ...
edger sva written 5.0 years ago by Brian Haas90 • updated 4.7 years ago by Gordon Smyth37k

Latest awards to Brian Haas

Great Question 5.0 years ago, created a question with more than 5,000 views. For RNA-Seq, generate batch-free count matrix
Student 5.0 years ago, asked a question with at least 3 up-votes. For RNA-Seq, generate batch-free count matrix
Popular Question 5.0 years ago, created a question with more than 1,000 views. For RNA-Seq, generate batch-free count matrix

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 316 users visited in the last hour