4 votes
Accepted

Extract sequence context of high-degree nodes in assembly graphs

I don't have a recommendation of specific tools, but we might be able to use the GFA file itself to get at this with just bash commands. For these examples I use the linked GFA here, which is a ...
Maximilian Press's user avatar
4 votes

Are there open-sourced graph-based variant callers?

Yes, there are. There are some suggestions in the comments (VG, WhatsHap, GraphAligner, Minigraph). However, to be clear, the current default variant calling algorithm used in the GATK (the haplotype ...
winni2k's user avatar
  • 2,266
3 votes
Accepted

Creating a scatterplot by a json data in js

It seems like you are already on the right track. The code you provided fetches the protein data from the JSON file and generates a scatter plot with D3.js based on two properties: ...
BigMistake's user avatar
3 votes

Extract sequence context of high-degree nodes in assembly graphs

Edit: I've written a short blog post describing my use of nodeSeqs.sh to investigate the functions of sequences at the nodes of short-read assembly graphs for a set of human oral microbiome samples. ...
acvill's user avatar
  • 613
3 votes
Accepted

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

Very quickly because I'm not around. I think I know what's going on, but don't have enough time to figure the df. The key thing is seaborn needs to know where ...
M__'s user avatar
  • 12.3k
3 votes

Can you style network visualizations of directed graphs using NETWULF?

I'm the author of gravis, an open-source package for interactive graph visualization in Python. It allows to draw directed graphs from NetworkX and the resulting visualization can be modified by user ...
Robert Haas's user avatar
2 votes
Accepted

In Pygraphviz, How can I assign edge colors according to edge weights?

This might help you ...
Mr_Z's user avatar
  • 629
2 votes
Accepted

Understanding regularization step in Meta-cell pre processing

Without looking in too much detail: We may suppose that $S$ is a matrix with dimensions indexed as $(i, j)$. So $s_{ij}$ is the cell of $S$ indexed to the $i$th row and $j$th column, and $s_{ji}$ is ...
Maximilian Press's user avatar
1 vote
Accepted

How to normalise the histogram height in matplotlib

One approach is density, traditionally the code would be ... ...
M__'s user avatar
  • 12.3k
1 vote

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

I'm not familiar with seaborn, but I'd guess from the error that there's at least one text value inside the Synergy_percent field that is encouraging the rest of ...
gringer's user avatar
  • 14.1k
1 vote

How to create Beta Diversity distance boxplot

You can use as.data.frame() or as_tibble() to convert/coerce your matrix to a data frame or a tibble respectively (Technically a ...
haci's user avatar
  • 4,112
1 vote

Construct the Overlap Graph of a Collection of k-mers

You will want to create a self loop for a $k$-mer $s$ whenever $s_1,...,s_{k-1} = s_2,...,s_k$. This will only happen when all of the characters of the $k$-mer are identical, as $s_1=s_2, s_2=s_3,...,...
Throckmorton's user avatar

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