Questions tagged [software]

Computer programs that aid in the storage, processing, and analysis of biological data.

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Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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797 views

Do blurry images cause eye strain? At what point is an image so blurry the eye stops trying to focus it?

I'm a user experience designer concerned about a new trend of blurring screens when showing a lightbox/dialog box over top (see below). From what I know, blurry images cause the brain to work hard ...
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1answer
64 views

What software do I need to read-write cas9? and .dna files?

I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually ...
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330 views

What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?

What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
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0answers
174 views

What software/approach to use to build a graph based on microarray gene expression correlation?

What software to use to build a graph based on microarray gene expression mutual correlation? I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
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211 views

How do I import FASTA files into Haploview?

I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software. I Have my sequences in a FASTA ...
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0answers
67 views

Open Source Variant Caller comparable to GATK Haplotype Caller?

Is there a Variant Caller comparable algorithmically and in performance to GATK Haplotype Caller but Open Source Compliant (non-restrictive use)?
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225 views

Workflow for batch analysis of ROI in histology samples

This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via ...
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12 views

Single cell lineage tracer

I need a Software or Python code or algorithm which can trace cell lineages. In my case the cells are budding yeast. I have already a segmentation python code and I only need to trace each cell.
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120 views

How to do Sliding 80mer Window search against a database with fasta

I know how to do a 80-mer window search against a single protein ...