Questions tagged [graphs]
The graphs tag has no usage guidance.
16
questions
1
vote
0
answers
29
views
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 ...
- 804
-2
votes
1
answer
95
views
Creating a scatterplot by a json data in js
I have a json file of protein data of mouse and human like
...
- 1,945
1
vote
0
answers
16
views
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 ...
- 123
0
votes
1
answer
18
views
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 ...
- 376
2
votes
1
answer
2k
views
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).
...
- 307
4
votes
2
answers
10k
views
Error in seaborn plot " Horizontal orientation requires numeric `x` variable"
I am trying to plot a box plot with seaborn with the following code
...
- 395
0
votes
1
answer
103
views
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.
- 103
10
votes
2
answers
229
views
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. ...
- 603
0
votes
0
answers
12
views
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 ...
- 1
0
votes
1
answer
204
views
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
0
votes
1
answer
878
views
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
1
answer
398
views
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 ...
- 371
0
votes
1
answer
437
views
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 :
...
- 21
2
votes
2
answers
424
views
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 ...
- 21
0
votes
0
answers
144
views
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, ...
- 39
2
votes
1
answer
138
views
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 ...
- 1,427