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Questions tagged [graphs]

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Are there efficient tools for PANGENOMES visualization (GFA size >2GB)?

I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most ...
AIsaac's user avatar
  • 23
3 votes
0 answers

How to do post hoc comparisons after a repeated measures ANOVA in R

I have a data set of several samples with their expression of proteins, in response to four different doses of a drug and two genotypes. I have been able to generate the two-way ANOVA using ezANOVA ...
Johnson's user avatar
  • 31
1 vote
1 answer

Constructing a pangenome graph using multiple samples

I am working with yeast strains (specifically S. cerevisiae) that have been cultured and evolved over many generations in the lab. I am using the reference S288C strain when I do certain analyses but ...
rimo's user avatar
  • 1,033
-2 votes
1 answer

Creating a scatterplot by a json data in js

I have a json file of protein data of mouse and human like ...
Zizogolu's user avatar
  • 2,232
1 vote
0 answers

analysing node connectivity difference in a continuous scale (edge weighted by correlations)

I have an edge list object weighted by a correlation value. I would like to know the changes in the node's connectivity on a continuous scale. In other words, how does the node connectivity differ ...
data's user avatar
  • 123
0 votes
1 answer

Understanding regularization step in Meta-cell pre processing

I'm reading through this paper: Baran, Y., Bercovich, A., Sebe-Pedros, A., Lubling, Y., Giladi, A., Chomsky, E., ... & Tanay, A. (2019). MetaCell: analysis of single-cell RNA-seq data using K-nn ...
Angus Campbell's user avatar
2 votes
1 answer

How to normalise the histogram height in matplotlib

I am trying to create a histogram plot with matplotlib. I am using bmi column from four different data frames (d1, d2, d2, d4). ...
Riya's user avatar
  • 307
4 votes
2 answers

Error in seaborn plot " Horizontal orientation requires numeric `x` variable"

I am trying to plot a box plot with seaborn with the following code ...
Megha's user avatar
  • 395
0 votes
1 answer

Is there a software that allows to convert a jpeg graph into dataset?

I have a very old graph as a .jpeg picture that I would like to convert into a dataset to be able to operate with it using R/python. I have no idea if it is even possible.
Mark's user avatar
  • 103
10 votes
2 answers

Extract sequence context of high-degree nodes in assembly graphs

I often use metaSPAdes to assemble short reads from human microbiomes. My simplified understanding of short-read de Bruijn graph assemblers is that they fail where ambiguous paths cannot be resolved. ...
acvill's user avatar
  • 613
0 votes
0 answers

Plant signaling pathway interconnections

I'm sorry for having such a juvenile question, but I'm still new in bioinformatics, and I was wondering whether there is any tool able to perform the task I'm dealing with now. Here is a short ...
Tom's user avatar
  • 1
0 votes
1 answer

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. ...
Apppii092's user avatar
0 votes
1 answer

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 ...
Apppii092's user avatar
1 vote
1 answer

Barplot without alphabetizing x-axis

I'm inputting a .csv file and then plotting a barplot based on the colnames but when I go plot the order the names are being alphabetized rather than get the order that is in the .csv file. How to I ...
mmpp's user avatar
  • 391
0 votes
1 answer

How to create Beta Diversity distance boxplot

I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object. I have a Morisita-horn distance generated by vegdist fonction : ...
Gaël.T's user avatar
  • 21
2 votes
2 answers

Construct the Overlap Graph of a Collection of k-mers

I am doing a course on graph algorithms in genome sequencing and the current assignment involves building an overlap graph from a bunch of k-mers. Formally the problem is as follows: Input: A ...
Gonzo's user avatar
  • 21
0 votes
0 answers

How to plot a graph of Linkage disequilibrium with limited information

I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, ...
Ugur Toprak's user avatar
2 votes
1 answer

Are there open-sourced graph-based variant callers?

I would like to compare GATK with graph-based variant callers. I have seen the Fast and accurate genomic analyses using genome graphs paper from SevenBridges and the paragraph tool by Illumina, though ...
0x90's user avatar
  • 1,447