User: Mike
Mike • 1.0k
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Posts by Mike
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C: Eigen genes using WGCNA
... This script will give you name of genes in each module ...
written 29 days ago by
Mike • 1.0k
0
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1
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Comment:
C: Eigen genes using WGCNA
... Agree with Kevin's point.
you can try with this code to extract modules..
**Extract modules**
module_colors= setdiff(unique(dynamicColors), "grey")
for (color in module_colors){
module=SubGeneNames[which(dynamicColors==color)]
write.table(module, paste("module_",color, ".t ...
written 4 weeks ago by
Mike • 1.0k
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... Hi All,
I am looking pipeline for analysis Lexogen QuantSeq 3' mRNA-Seq data. I will be very grateful if you help me.
regards ...
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... I found a nice tutorial to build Phylogenetic Trees from fasta sequence...
http://www.cbs.dtu.dk/courses/biosys/binfintro/phylogeny.php
Step 1: Open the sequence file (fasta), select the entire file, and copy the sequences.
Step 2 : Align the sequences in using the mafft server at EBI with def ...
written 8 weeks ago by
Mike • 1.0k
0
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2
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475
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... Thanks cpad0112, yes I can read file in read.phylip function from phylotools but not from ggtree/ treeio. How can I build tree using this phylip file in phylotools. ...
written 8 weeks ago by
Mike • 1.0k
0
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2
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475
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... Thanks Sej, thats my problem, how to generate phylip file (phylip alignment + newick string) to plotting in ggtree. ...
written 8 weeks ago by
Mike • 1.0k
0
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2
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475
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... Thanks jrj.healey for your help, I have around 150 protein sequences, this is just toy/example data. ...
written 8 weeks ago by
Mike • 1.0k
0
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2
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475
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2
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... >proteinsA
-------------------------------MGDSRDLCPHLDSIGEVTKEDLLLKSKGT
CQSCGVTGPNLWACLQVACPYVGCGESFADHRT-------DKKPA-----LCKSY-----
------QKLVSEVWHKKRPSYVVP-----
>proteinsB
MTGSNSHITILTLKVLPHFESLGKQEKIPNKMSAFRNHCPHLDSVGEITKEDLIQKSLGT
S--------------HVSFP----------- ...
written 8 weeks ago by
Mike • 1.0k
0
votes
2
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475
views
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... It is not copied and pasted file , I downloaded from from EMBOSS seqret result page as per below...
![enter image description here][1]
I have also MAFFT (alignment file) file but dont know how to use this file for generate tree.
[1]: https://s8.postimg.cc/vqh06ewat/image.jpg ...
written 8 weeks ago by
Mike • 1.0k
4
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2
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6 follow
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... Hi all,
I have fasta sequence of some proteins and I want to convert fasta format to phylip file format to build phylogenetic tree using ggtree. I tried online EMBOSS seqret tool to convert fasta file to phylip format but I got error when i read in ggtree.
my input sequence
>proteinsA
...
written 8 weeks ago by
Mike • 1.0k
• updated
5 weeks ago by
Guangchuang Yu • 2.0k
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