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Bioinformatics : Recent Questions and Answers (Page 5)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in...

Asked on 10/03/2021

1 answer

How to create Phylogenetic Trees from fasta files in Python or R?

I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in...

Asked on 10/03/2021

4 answer

Help with setting DimPlot UMAP output into a 2x3 grid in Seurat

On my merged seurat object of 6 samples, when I use the split.by function in tandem with the Dimplot/UMAP plot, all six samples are displayed in series along a commonly...

Asked on 10/03/2021

1 answer

"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine...

Asked on 10/02/2021 by Pragati Bhingare

0 answer

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there are listed patterns for alleles,...

Asked on 10/01/2021 by Guy Coder

1 answer

Determining significance of a variable in a glm model

How would one determine the significance of a variable in a glm model? If I, for example, have a dataframe like seen below, how would I determine if the origin...

Asked on 09/30/2021 by RMM

2 answer

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11...

Asked on 09/30/2021

1 answer

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} =...

Asked on 09/28/2021 by Gogis

2 answer

How can I take cell number into account to find total RNA expression?

I'm hoping to quantitatively show differences in total RNA expression for a gene in a cluster of interest between different experimental groups. My exported average RNA values for each experimental...

Asked on 09/27/2021 by user9283

2 answer

Specific cell type identification in Single Cell Sequencing

In order to define which cell is of which type we need to identify a set of rules, for instance neurons should express one of the following: Thy1, Rbfox3, MAP2,...

Asked on 09/27/2021

4 answer

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