Moderator: Jean-Karim Heriche

Reputation:
16,570
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
2 hours ago
Joined:
7 years, 4 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 2,084 results • page 1 of 209 • next >
2
votes
1
answer
5.4k
views
1
answers
Answer: A: Network plot from expression data in R using igraph
... Also, as a complement, check out this [tutorial on network visualization with R][1]. [1]: http://kateto.net/network-visualization ...
written 4 days ago by Jean-Karim Heriche17k
1
vote
2
answers
312
views
2
answers
Answer: A: How to determine the surface markers in a gene list
... In addition to previous suggestions of looking for relevant protein domains and GO annotations, you could also check which of the proteins in your list are known or putative cell surface proteins in the following databases: - [cell surface protein atlas][1] - [extracellular matrix interaction d ...
written 4 days ago by Jean-Karim Heriche17k
5
votes
2
answers
120
views
2
answers
Answer: A: Determination of hub genes in PPI network
... A hub is a node that has a higher degree than other nodes in the graph. How this translates in practice seems to vary between papers. Some just use an arbitrary threshold either as a fixed number or as a percentage, others choose a threshold based on some statistical argument e.g. outliers in the di ...
written 5 days ago by Jean-Karim Heriche17k
0
votes
1
answer
70
views
1
answers
Comment: C: Correlation mutual rank calculation
... You can do it in RStudio as long as your computer does have enough RAM. The main issue will probably be the time it takes to read the file. ...
written 5 days ago by Jean-Karim Heriche17k
1
vote
1
answer
70
views
1
answers
Answer: A: Correlation mutual rank calculation
... The correlation ranks have to be calculated relative to each gene separately. Try something like this: R <- matrix(NA, nrow = number.of.genes, ncol = number.of.genes) # Compute correlation ranks for each gene for(i in 1:number.of.genes) { # Rank all genes relative to gene ...
written 6 days ago by Jean-Karim Heriche17k
6
votes
2
answers
261
views
2
answers
Answer: A: What would be the trend in next few years in NGS era?
... The future is in data integration. Sequences are not going to be highly valuable on their own for very long but will be just one piece of data to use among others. From my perspective, sequencing, and other omics technologies, are moving to the microscope. Now that you can get sequence information f ...
written 6 days ago by Jean-Karim Heriche17k
3
votes
1
answer
61
views
1
answers
Answer: A: What are the differences between Gene Regulatory Network and Protein-Protein Int
... A gene regulatory network, as the name implies, is a network (i.e. a directed graph) in which the nodes are genes and the edges represent some form of regulatory action of one gene on another (usually activation or repression). A protein-protein interaction graph is typically an undirected graph whe ...
written 6 days ago by Jean-Karim Heriche17k
1
vote
0
answers
75
views
0
answers
Comment: C: Transcriptomic profile fluctuation between different time point
... Today and tomorrow don't define time points very precisely. I can imagine that today, you take a sample two hours after the patient has taken their medication but tomorrow, you'll take the sample just before. This is also without taking into account the effect that taking the first sample can have o ...
written 7 days ago by Jean-Karim Heriche17k
1
vote
0
answers
75
views
0
answers
Comment: C: Transcriptomic profile fluctuation between different time point
... You can almost never be sure a single measurement is representative because of all sources of variation such as biological and measurement noises. This is why there are replicates in a study. You should define what a time point is because how precisely/reproducibly you sample from a "time point" can ...
written 8 days ago by Jean-Karim Heriche17k
1
vote
1
answer
67
views
1
answers
Answer: C: secretome P error
... Missing features could indicate that some features couldn't be computed. One possible reason is that you didn't install software required to compute them. See the docs for secretomeP. One another note, it seems that using secretome P (that has been trained with mammalian proteins) for non-mammalian ...
written 8 days ago by Jean-Karim Heriche17k

Latest awards to Jean-Karim Heriche

Appreciated 3 days ago, created a post with more than 5 votes. For A: Why learn programming in bioinformatics?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 4 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 6 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: Why learn programming in bioinformatics?
Appreciated 6 days ago, created a post with more than 5 votes. For A: Why learn programming in bioinformatics?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 23 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Why learn programming in bioinformatics?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Why learn programming in bioinformatics?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Appreciated 11 weeks ago, created a post with more than 5 votes. For Heatmaps in R
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Great Question 3 months ago, created a question with more than 5,000 views. For Heatmaps in R
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How to make sure there is no duplicate sequence in a fasta file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1504 users visited in the last hour