User: David Westergaard

Reputation:
1,380
Status:
Trusted
Location:
Copenhagen, Denmark
Last seen:
1 year, 9 months ago
Joined:
6 years, 10 months ago
Email:
d****@harsk.dk

I should write something here at some point, I guess.

Posts by David Westergaard

<prev • 156 results • page 1 of 16 • next >
4
votes
3
answers
6.6k
views
3
answers
Answer: A: dispersion of a gene, what does it mean?
... The dispersion is sometimes a synonym for the variance, but not in this case. DESeq assumaes a negative binomial distribution, which has two parameters: mean and dispersion. The dispersion is a parameter describing how much the variance deviates from the mean. The Poission distribution is sometimes ...
written 3.2 years ago by David Westergaard1.4k
0
votes
1
answer
644
views
1
answers
Comment: C: Best way to check posttranslation mod-s?
... Have you tried simply looking up the protein at http://uniprot.org? ...
written 3.5 years ago by David Westergaard1.4k
2
votes
4
answers
1.4k
views
4
answers
Answer: A: Protein location by gene name
... http://compartments.jensenlab.org allows you to look up each gene individually, or download a flatfile with the location of each. ...
written 3.5 years ago by David Westergaard1.4k
0
votes
2
answers
2.7k
views
2
answers
Comment: C: Protein Sequence Clustering (CD-HIT vs BLASTClust + Problems in BlastClust)
... Have you tried to simply increase the identity threshold when using CDhit? Also, what is the biological reasoning behind clustering? It sound like these sequences are already highly similar. Are you trying to divide them by certain mutation or something? ...
written 3.5 years ago by David Westergaard1.4k
3
votes
2
answers
994
views
2
answers
Answer: A: Database that has all known proteins associated with a particular PFAM or TIGRFA
... UniProt sounds like the solution you are looking for. The examples below works for both pfam and TIGRFAM, and you can use logic. E.g. PF02171 OR TIGR00008.   Web results: http://www.uniprot.org/uniprot/?query=PF02171&sort=score Downloadable/programmatic: http://www.uniprot.org/uniprot/?query= ...
written 3.5 years ago by David Westergaard1.4k
3
votes
0
answers
1.6k
views
0
answers
Comment: C: What to write in the y axis of RNA-Seq plot
... You are overthinking it. If what you show for RNA-Seq is the FPKM count, write that. You should always adhere to the KISS principle when creating and labeling plots. ...
written 3.5 years ago by David Westergaard1.4k
2
votes
1
answer
4.1k
views
1
answers
Comment: C: True/False Positives/Negatives in R
... Coming up with negatives is always difficult. The genes you are referring to, are these the ones that "genes that based on a condition have nothing to do with the complex" as you state? If so, it should be fine. The most important part is always writing up exactly what you consider your positive and ...
written 3.9 years ago by David Westergaard1.4k
0
votes
0
answers
1.0k
views
0
answers
Comment: C: Does these algorithms need to train to estimate genetic network?
... Your question does not make sense. A genetic algorithm is an optimisation algorithm. What are you optimising? I don't even know what a boolean algorithm is. What is a "genetic network"? ...
written 4.2 years ago by David Westergaard1.4k
0
votes
0
answers
1.0k
views
0
answers
Comment: C: Using reactome.db for finding genes interaction
... It is not quite clear what you are looking for. Do you want to find out which domains in the proteins are interacting, or just if the proteins are interacting? If you just google database of interacting protein domain there are plenty of options, and this covers the first option. If you would like t ...
written 4.2 years ago by David Westergaard1.4k
1
vote
1
answer
3.1k
views
1
answers
Comment: C: Fast generation of random scale-free networks with a defined power law using R
... Honestly, a simple re-wire algorithm for that problem should not be that slow. The task can easily be split over multiple threads and you can just save the resulting random graph if you need it for later analysis.  Before concluding the network is scale-free please read http://arxiv.org/abs/0706.10 ...
written 4.2 years ago by David Westergaard1.4k

Latest awards to David Westergaard

Commentator 3.5 years ago, created a comment with at least 3 up-votes. For C: What to write in the y axis of RNA-Seq plot
Scholar 3.5 years ago, created an answer that has been accepted. For A: Identify enzymes among a list of Uniprot ACs
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Small molecule databases
Scholar 3.5 years ago, created an answer that has been accepted. For A: Identify enzymes among a list of Uniprot ACs
Scholar 4.2 years ago, created an answer that has been accepted. For A: Identify enzymes among a list of Uniprot ACs
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Where Can I Find Some Agilent Sample Cel Files
Scholar 4.3 years ago, created an answer that has been accepted. For A: Identify enzymes among a list of Uniprot ACs
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Where Can I Find Some Agilent Sample Cel Files
Guru 4.3 years ago, received more than 100 upvotes.
Scholar 4.8 years ago, created an answer that has been accepted. For A: Identify enzymes among a list of Uniprot ACs
Centurion 4.9 years ago, created 100 posts.
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Disease Pathways Database
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Search The Protein Domain By Sequence In Batch Work
Appreciated 5.5 years ago, created a post with more than 5 votes. For A: Search The Protein Domain By Sequence In Batch Work
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Where Can I Find Some Agilent Sample Cel Files
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: How Are The Test_Stat, P-Value, Q-Value Calculated In The Cuffdiff Output
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: List Of Naturally Occuring Metabolites/Compounds In Eukaryotes ?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Confusion In Pdb File Format
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Where To Find Annotation File For Agilent Microarray?
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Is There Any Website To Get Cellular Location Information For A List Of Genes?
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Test Tool That Can Compare Multiple Gene Lists

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2035 users visited in the last hour