User: Jake Warner

gravatar for Jake Warner
Jake Warner810
Reputation:
810
Status:
Trusted
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Website:
https://2-bitbio.com/
Twitter:
@ScientistJake
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 5 months ago
Email:
w***********@gmail.com

Posts by Jake Warner

<prev • 102 results • page 1 of 11 • next >
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Comment: C: RepeatModeler nseg installation problem
... Here's the errors: https://pastebin.com/LfsaNdmF All the errors relate to `non-void` functions. ...
written 13 months ago by Jake Warner810
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Comment: C: RepeatModeler nseg installation problem
... I think I have a hackaround working: https://github.com/ScientistJake/nseg_osx ...
written 13 months ago by Jake Warner810
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Comment: C: Alternatives to RepeatModeler / nseg install fail
... Apparently the conda package doesn't work? From RepeatModeler github: "WARNING: There is a bioconda and a docker package floating around proporting to have a functional RepeatModeler package. Neither work correctly. For the time being we recommend installing this program as described below." ...
written 17 months ago by Jake Warner810
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Alternatives to RepeatModeler / nseg install fail
... Dear All, I am gearing up for a genome annotation run using MAKER. It is suggested to use a repeat library when running MAKER and as such I am trying to set up [RepeatModeler][1] to do so. RepeatModeler relies on program (among several others) called [nseg][2] for which I cannot find any documenta ...
annotation maker written 17 months ago by Jake Warner810 • updated 8 months ago by Juke344.5k
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Answer: A: Is there any alternative for CD_Hit to remove redundancy from asemmbled trinity
... Getting 'unigenes' from Trinity assemblies is tricky business. I've found that [Corset][1] performs better than CD-Hit. Another idea is to BLAST all the transcripts and group them by reciprocal best blast hit. [1]: https://github.com/Oshlack/Corset/wiki ...
written 2.1 years ago by Jake Warner810
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Answer: A: local web BLAST server
... It doesn't email but I've found [sequence server][1] to be very useful as a local blast server. [I also wrote one][2] that runs on R-shiny to which you could easily add the mail tool from Sej Modha's comment. Just change the output to a txt and send that as the mail message. [1]: https://www ...
written 2.1 years ago by Jake Warner810
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Comment: C: WGCNA network with condition and normal samples
... Hi, You are correct, the genes which are regulated by the treatment will move as a group and show up as a module. But even if most of the genes move they wont move in the same *way* and you will detect multiple modules (I'm oversimplifying a bit here). A big factor is the number of samples overall ...
written 2.1 years ago by Jake Warner810
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Comment: C: Problem for understanding the number of modules in construction network based on
... Hi Modzari, This is more of an R problem and less of a WGCNA or RNAseq/array problem. What the code you pasted does, is import an annotation file which is a series of columns with gene name, probe name, genomic coordinates etc, and associate those annotations with the results of the correlation tes ...
written 2.1 years ago by Jake Warner810
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Answer: A: WGCNA network with condition and normal samples
... Hi, WGCNA is unsupervised in the network construction and phenotypic data is used for post hoc correlation tests. So in basic terms all the expression data is fed in at once and if a group of genes responds specifically to one treatment they should be detected as a module and correlate with the sa ...
written 2.1 years ago by Jake Warner810
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Answer: A: Problem for understanding the number of modules in construction network based on
... Hi, `blockwiseModules` stores the module assignments in `colors`. So to count the modules you can see how many levels are in the `colors` vector: my_network <- = blockwiseModules(datExpr, ...) module_assignments <- my_network$colors #count the modules nlevels(factor(m ...
written 2.2 years ago by Jake Warner810

Latest awards to Jake Warner

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Confusion regarding WGCNA
Centurion 13 months ago, created 100 posts.
Popular Question 16 months ago, created a question with more than 1,000 views. For Change paired end library from FR to RF
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Scholar 2.1 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Supporter 2.6 years ago, voted at least 25 times.
Scholar 2.7 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 2.9 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 2.9 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 3.1 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: 3D PCA issue
Rising Star 3.2 years ago, created 50 posts within first three months of joining.
Scholar 3.3 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data
Scholar 3.4 years ago, created an answer that has been accepted. For A: WGCNA dealing with missing data

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