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Questions tagged [matrix]

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How to import the average expression matrix for all detected genes in each cluster into Seurat?

I download a matrix which has 19 columns and the first column is gene names, other is cell cluster: In fact, I just want to plot the feature plot which like this: My idea is to use the function <...
Bioinfotec's user avatar
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1 answer

conducting a ttest on a board of 1000 genes in 50 peope divided into to groups(A and B). pvalues are different each time

I am struggling in conducting at test on a board of 1000 genes in 50 individuals divided into to groups (A and B). I have a dataset of 1000 genes of two groups of people (total individuals=50) group A ...
biostefania's user avatar
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Making a matrix when samples that have missing data

I am trying to make a dataset for methylation analysis. I called methylation using Methyldackel and there are various positions without methylation calls. This creates a problem because when I try to ...
Desmodus1984's user avatar
2 votes
1 answer

Compare substitution matrices

I am looking for methods to compare substitution matrices to determine which one is better for a given set of data / type of protein. Do you know such methods / tools? e.g. BLOSUM62 vs PHAT for 50k - ...
maciejwww's user avatar
  • 237
1 vote
1 answer

DNA, molecular descriptors

Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA. Thanks in advance!
Balint Biro's user avatar
1 vote
1 answer

Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

I have a couple of prokaryotic genes that I'm trying to build phylogenetic trees from. I inputted them into IQTree, which, as part of the workflow, runs through multiple substitution models until it ...
Laura's user avatar
  • 937
1 vote
1 answer

How to assess if this strategy is good to have some phylogenetic information?

I have several organisms and I want to calculate for each one of these their codon composition implementing a pairwise distance matrix between these codon vectors to build a phylogenetic tree. ...
Spartan 117's user avatar
4 votes
2 answers

Motivation behind the neighbor-joining distance matrix recomputation

In each iteration of the neighbour-joining method of phylogenetic trees construction, after joining the nearest neighbours the (additive) distance matrix $D_{m \times m}$ is recomputed as $$Q_{ij} = (...
Gogis's user avatar
  • 143