User: vincentpailler

gravatar for vincentpailler
Reputation:
100
Status:
Trusted
Location:
Last seen:
6 days, 10 hours ago
Joined:
1 year, 3 months ago
Email:
v*************@hotmail.fr

Posts by vincentpailler

<prev • 112 results • page 2 of 12 • next >
0
votes
2
answers
255
views
2
answers
Comment: C: Problem to run checkm.
... I checked the documentation about this package and I think I did good ... My files are in the good format and the command line I used looks good. ...
written 5 months ago by vincentpailler100
0
votes
2
answers
255
views
2
answers
Comment: C: Problem to run checkm.
... Yes I tried but I always get the same results.. I don't understand why ...
written 5 months ago by vincentpailler100
3
votes
2
answers
255
views
5 follow
2
answers
Problem to run checkm.
... Hello, I have several files which contain proteic fasta sequences. Each file correspond to a cluster of genes. UniRef90_100.fasta UniRef90_101.fasta UniRef90_102.fasta UniRef90_103.fasta UniRef90_104.fasta UniRef90_105.fasta UniRef90_10.fasta UniRef90_11.fasta U ...
fasta contamination checkm written 5 months ago by vincentpailler100 • updated 5 months ago by Asaf6.5k
0
votes
1
answer
267
views
1
answers
Comment: C: Community detection in R thanks to the igraph package
... Thanks for your reply. The biggest component I get is always the first one (whatever the dataset I import) . So I am going to apply clustering on this one. I use : `genomes<-split(names(V(g)), components(g)$membership)` , and I extract the first component with `big_one<-genomes[[1]]` . Is th ...
written 5 months ago by vincentpailler100
0
votes
1
answer
267
views
1
answers
Comment: C: Community detection in R thanks to the igraph package
... Could the connected components (subgraph) of the graph give me back reconstructed genomes ? In your opinion, I should first extract each subgraph, and then, apply clustering algorithms on each of them in order to "improve" the exactness of the reconstructed genomes? ...
written 5 months ago by vincentpailler100
3
votes
1
answer
267
views
1
answer
Community detection in R thanks to the igraph package
... I have a data.frame with the correlations between OTUs and genes. These correlations will allow me to construct genomes. This data.frame has 1105854 rows. var1 var2 corr 1 OTU3978 UniRef90_A0A010P3Z8 0.846 2 OTU4011 UniRef90_A0A010P3Z8 0.855 3 OTU4929 UniRef ...
R network community igraph written 5 months ago by vincentpailler100 • updated 5 months ago by Jean-Karim Heriche21k
0
votes
0
answers
326
views
0
answers
Comment: C: How to reduce my dataset in order to plot it?
... That's what I meant. I applied clustering on the matrix which corresponds to my giant component, and I get back only one cluster. Maybe I don't understand your draft.. I can extract each connected component, make the matrix for each of them and then apply clustering. When you say " You have to apply ...
written 5 months ago by vincentpailler100
0
votes
0
answers
326
views
0
answers
Comment: C: How to reduce my dataset in order to plot it?
... By the way, when I apply different clustering methods (biclustering, kmeans) , I will get only one cluster, which corresponds to my giant component. I don't know how to apply a "real" clustering on it. ...
written 5 months ago by vincentpailler100
0
votes
0
answers
326
views
0
answers
Comment: C: How to reduce my dataset in order to plot it?
... The dataframe I extract from the giant component looks like this (it is only the head) : var1 var2 corr 1 OTU3978 UniRef90_A0A010P3Z8 0.846 2 OTU4011 UniRef90_A0A010P3Z8 0.855 3 OTU4929 UniRef90_A0A010P3Z8 0.829 4 OTU4317 UniRef90_A0A011P550 0.850 5 ...
written 5 months ago by vincentpailler100
0
votes
0
answers
326
views
0
answers
Comment: C: How to reduce my dataset in order to plot it?
... I found the package `biclust` which could be interesting to apply clustering on my giant component. The problem is that I have my data in the form of data.frame rather than matrix. Do you know this package, and if yes, if it could be suitable to my data.set and my analysis? ...
written 5 months ago by vincentpailler100

Latest awards to vincentpailler

Popular Question 3 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping
Centurion 5 months ago, created 100 posts.
Popular Question 9 months ago, created a question with more than 1,000 views. For Mapping vs Quasi-Mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1773 users visited in the last hour