Questions tagged [networks]
The networks tag has no usage guidance.
63
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2
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65
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Coexpression network analysis
I have a question related with the most popular frameworks for network construction: WGCNA for weighted networks and igraph package for unweighted networks.
What are the advantages or disadvantages of ...
- 53
0
votes
1
answer
82
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How to find closely related genes for a specific gene from WGCNA modules?
I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules.
Among all ...
- 43
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0
answers
16
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Running hubCheck utility from inside K8s's Pod
I'm trying to run hubCheck utility* from inside Kubernetes Pod but for some reason I get this Network error:
...
- 111
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votes
1
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174
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Can you style network visualizations of directed graphs using NETWULF?
I want to draw directed graphs using networkx, followed by manual tuning of the visualization with the use of NETWOLF.
Here is the example of a network.
...
- 27
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1
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749
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In Pygraphviz, How can I assign edge colors according to edge weights?
I am now drawing a weighted directed graph using Pygraphviz.
The adjacency matrix A of the weighted directed graph is
...
- 27
1
vote
0
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20
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How to find disease association of disgenet with string db in homo sapiens
I want to work string-db to read the protein-protein interaction from it and I look up disease association from disgenet but the Ids do not seem to match-up and I do not know what to do.
for example ...
- 111
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0
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102
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Network analysis: confidence score (STRING database) validation
I am working on network analysis of differentially expressed genes, but the problem I am facing is that the gene set is very small (around 16 genes only), so when I'm trying to build an interaction ...
1
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0
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18
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How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?
I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
0
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2
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372
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STRINGdb: reverse map STRING identifiers to gene names?
Is there a functionality within STRINGdb package or in another environment to reverse map the STRING identifiers to Gene names?
For example, the entire STRING network can be downloaded using the ...
- 428
1
vote
2
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70
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Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?
I am currently working on a network pharmacology project where I am supposed to find out the possible diseases our drug might have an effect on. I am not a bioinformatics student, so my knowledge in ...
- 11
2
votes
1
answer
143
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Metapath2vec on Drug-ADR Heterogeneous Graph
I am new in this field and I am having some problems regarding a new project.
I built a graph using Drugbank Data connected to SIDER Adverse Reactions.
I used Organ- level Terms to classify the ADRs ...
- 21
2
votes
1
answer
57
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Populations genetics and dynamics of bacteria on a Graph
Disclaimer:
I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense.
My purpose:
I would like to simulate genetic evolution of bacterial populations, ...
- 123
4
votes
1
answer
243
views
How to calculate module-trait relationship when trait data is in binary format?
I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
- 43
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0
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61
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Regarding RNA seq data analysis and building coexpression network
I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot.
I am currently normalizing RNA seq data for comparing genes expression within and between samples. ...
- 11
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votes
1
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143
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What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)?
What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)?
Barycenter scores are calculated as 1 / (total distance from vertex v to all other vertices) in a strongly ...
- 103
1
vote
1
answer
272
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Importing a WGCNA co-expression network into a networkX graph in Python
Is there a way to generate a WGCNA co-expression graph in R, and then to import that graph into Python such that I can represent it using a networkX object?
1
vote
1
answer
48
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how to evaluate neural networks
I have made some architectures of neural networks in order to classify proteins in three categories. I have calculated true positive, true negative, false negative, false positive, Mathews, ...
- 101
2
votes
1
answer
179
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Identifying mutually **exclusive** gene sets
I am interested in identifying gene pairs (or better: sets of genes) whose expression is mutually exclusive.
Ideally, both genes (or gene sets) would be widely expressed but I am also interested in ...
0
votes
1
answer
2k
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WGCNA: Problem with selecting soft threshold
I have 25 tumor samples with counts data. Initially, I filtered out low expressed genes and then converted counts to varianceStabilizingTransformation using ...
- 621
1
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1
answer
54
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Random networks in PPi
I am working with an in silico model to measure the distances between drugs targets and disease proteins of a disease. I would want to compare these distances with the distances of random networks but ...
-1
votes
1
answer
66
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Module preservation and hub genes finding
I ran module preservation analysis between two condition and on the basis of preservation z summary i would to go for downstream analysis.So I m interested in looking for hub-genes of those modules ...
- 1,694
2
votes
1
answer
101
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Visually summarizing phylogenetic networks
After having worked with Bayesian phylogenetic tree inference for some time, I am now trying out a method to infer network phylogenies. To get an idea of what it infers, I'd like to find a way of ...
- 121
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votes
2
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194
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Proteomics data Vs Transcriptomics data?
I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
- 145
1
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0
answers
59
views
How to write the subclusters in file?
I have constructed a gene co-expression network from RNA-seq data. The network file is in edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs ...
-1
votes
2
answers
325
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How I debug this code?
I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error
...
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1
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1
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593
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Clustering of gene co-expression network by igraph R package
I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges.
The network file as an edge list format of memory around 1gb ...
0
votes
1
answer
271
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How do I get the adjacency matrix from gene similarity network?
I am exploring application of Graph convolution network on gene similarity network. I am trying to explore
genemania.org and https://string-db.org/
Please let me know where can I find the data for my ...
Susha Suresh
1
vote
0
answers
40
views
Kinetics "Master Equation"
In stochastic (probabilistic) models, the evolution of a system over time is calculated using a "Master Equation" which also factors the external and internal noise / perturbations in order ...
- 103
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votes
1
answer
100
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Attractor Landscape Analysis
I have come across a modeling toolbox, ATLANTIS, which is able to determine cell fates in silico based on the input models provided. This MATLAB-based toolbox is built on a method called "Attractor ...
- 103
1
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1
answer
47
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Retrieving Metabolic networks from WIT Database
How can I get the dataset for all the 43 metabolic networks for this paper:
https://www.nature.com/articles/35036627
It looks like the WIT database does not exist anymore.
- 15
4
votes
3
answers
753
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Error while loading a big file with Cytoscape
I installed Cytoscape 3.7.1 with java 1.8.0_191 in windows server 2012. I have a 7.4 GB csv file (about 1,500,000 reords) and when I tried to load it into the ...
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2
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48
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Visualize similar interactions in two homologous networks
Background
I have two networks with homologous genes from two different species.
To identify homologs I performed a functional comparison. One of the species is not well studied while the other one is ...
- 297
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1
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65
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How to create a graph of multi column gene dataset?
well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes :
and this is ...
- 129
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0
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49
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What are fundamentals to work on bioinformatic data analysis ? [closed]
Well, I'm a MSc student in Information Technology Engineering, trying to become more familiar in the Complex networks specially Bioinformatic field to get more knowledge of cancer detection by ...
- 129
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votes
1
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116
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Compare two networks of the same genes between two species
I had a set of genes for honey bees. I found the homologues of those genes in the house fly and created a network of the honey bee genes and a network of the homologous fly genes using STRING.
I ...
- 297
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2
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36
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Comparing between different set of clusters produced from the same network
I have a set of eight gene clusters which I obtained from clustering a network. However, I had to update the genes in the network at a later stage which lead to certain deletions (genes not present in ...
- 297
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1
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165
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How to calculate Gene Ontology terms in python
I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some ...
- 109
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votes
1
answer
34
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Check if a set of genes fall more on a specific cluster than other clusters
I have a network which I clustered into 11 smaller clusters. I have a set of genes and I would like to check if statistically significant number of these genes fall on any specific cluster. One method ...
- 297
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0
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1k
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How to format the Nexus file to create geographical maps with haplotypes in PopArt?
I'm trying to create a map in PopArt that allows me to visualise the distribution of several species. These are my Traits (=species) and GeoTags blocks:
...
- 309
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votes
2
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262
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Visualize network (graph) using "line" layout
I want to visualise a network in a way that the nodes are along a line (and the edges are not on that line).
I have included a simple example below.
Which network visualisation programs (Cytoscape, ...
- 2,604
7
votes
2
answers
160
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Are gene names same across species?
I have a bunch of gene names of Apis mellifera (specifically 194). I used these gene names as an input on STRING database to create a network for Drosophila melanogaster. 54 of those genes were also ...
- 297
2
votes
1
answer
224
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Negative scale-free topology
I am trying to build gene co-expression networks with WGCNA by combining in-house and publicly available RNA-seq datasets. I am interested in identifying gene networks associated with different ...
- 31
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0
answers
57
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The slopes of gene networks
I have a gene network that I clustered into 8 parts. I calculated the degree distribution of the clusters using Cytoscape and the slope of the clusters range from $0.7$ to about $1.3$.
From ...
- 297
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votes
1
answer
158
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Network comparison of single cells (from sequencing data)
What methods can we use to compare networks (PPI, gene regulatory etc) created from single-cell gene expression (or proteomics) data?
There are methods that construct networks by comparing two ...
- 2,604
1
vote
1
answer
150
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Motif Discovery in Bipartite networks using Cytoscape
I am trying to find over-expressed motifs in a bipartite transcription factor gene network.My genes are not very well characterized, so finding functional motifs has been a challenge. I used the motif-...
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344
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Create gene network from list of genes
This has also been posted on biostars
I had an initial bipartite transcriptional regulatory network for bees. My idea is to create a similar network for termites so as to check if similar genes are ...
- 297
2
votes
1
answer
597
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Program to make a haplotype network for a specific gene
Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. I would like to know how to generate the graph structure (i.e. the links between vertices), ...
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1
answer
53
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How to read gene regulatory network edge list files?
The following is an excerpt from an edge list file from the Gene Regulatory Database, YeastNet v3
...
- 139
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0
answers
94
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Locate KEGG/Reactome pathways in user defined network
I am working on big networks of genes. I want to locate KEGG/Reactome pathways in my network. I have already tried cytoKegg and ReactomeFI (Plugins of Cytoscape), they only give me a list of Pathways ...
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294
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How to simulate biological pathways?
I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using ...
- 1,417