Making Network Diagram From Pairs Of Gene Names

I want to make a network diagram from a list of gene pairs and their properties:

A B X
B C Y
A D Z

python cytoscape

• 2,510 views • link

updated 12.1 years ago by Biostar

• written 13.3 years ago by Pappu

Please edit your post to clarify your question or will be deleted.

• 0 views • link

written 13.3 years ago by JC

1 answer

Cytoscape will display this network. The format is A, relationship, B - where A and B will be your genes (nodes) connected by a given relationship (edge). Cytoscape can accept a .txt file.

• 15 views • link

written 13.3 years ago by Larry_Parnell

More posts like this

Batch-correction of partially confounded RNA-seq data
written 5.4 years ago by James Ashmore

Say I have RNA-seq data from 3 conditions (A,B,C) and a single batch (X) X A 2 B 2 C 2 I then decide that …
To keep the model of minimum p-value from the file
written 6.5 years ago by khn

Hello My file lists a millions of SNPs with their p-values by additive, dominant, and recessive models. I want to keep the SNPs with a …
To keep the model of minimum p-value from the file
written 6.5 years ago by khn

Hello My file lists a millions of SNPs with their p-values by additive, dominant, and recessive models. I want to keep the SNPs with a …
Assembling a sequence from the pairs of letters (X,Y)
written 8.1 years ago by Bogdan

Dear all, Please could you advise on an algorithm that could solve a relatively easy problem (I have just started recalling and reviewing very old …
Linking unique ID pairs
written 10.0 years ago by floris.barthel •

Hi! I'm trying to link together pairs of unique IDs using R. Given the example below, I have two IDs (here ID1 and ID2) that …
Network Diagram Of Protein Domain Architectures
written 12.3 years ago by Pappu

I have a protein domain which can be associated with various other domains. I got a list of these architectures: <pre><code>A B C A A …
Scatterplots Showing Correlation Between Gene Pairs
written 12.9 years ago by spaul8505 •

I have two dataframes <pre><code> x<-data.frame(matrix(rnorm(1000), nrow=1000, ncol=10)) y<-data.frame(matrix(rnorm(1000), nrow=1000, ncol=10)) </code></pre> where the rows are the genes and the columns are samples. I wanted …
Correlation On A List Of Lists
written 12.9 years ago by suganyasivagurunathan •

I have two list of lists A and B, A and B contain 100 data frames each and the dimension of each data frame is …
Row And Column Names In A Matrix
written 13.1 years ago by deschisandy •

I have the matrix in the following form: <pre><code> A-B A-C A-D A-E B-C B-D B-E C-D C-E D-E GENE 1 GENE 2 GENE 3 …
How Can I Generate A Venn Diagram In R For A Given Csv File
written 13.3 years ago by Payal •

Hello, AIM is to check common names between A and B or A and multiple variables I have a CSV file which looks like this... …