Motivation Given the interesting results found during the previously posted ChatGPT work, there was some sentiment that the python script that I had consolidated from that session might be reusable if it were generalized. I used this as an opportunity to explore creating a NextFlow pipeline, taking that python script...
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Using ChatGPT to explore thermal resilience based on gene counts
Intro This post has two motivations: Demonstrate using ChatGPT’s specialized Data Analyst model to explore a problem starting with the initial problem statement, showing dialog, generated code (often much modified by me). This section is quite long, but I’d be interested in your thoughts about the options it suggests in...
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PCA for gene count comparison between NCBI Crassostrea gigas Annotation Release 101 and GCF_963853765.1-RS_2024_06 reference genomes
12-23-2024
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Compare genes after CGI id conversion attempt 1
In order to get 1:1 matching between genes in Roberto’s gene counts matrix and Emma’s gene counts matrix, they need to be the same type of identifier. Most genes in Emma’s are “LOC” and Roberto’s are “CGI”
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Exploring nf-core differential abundance workflow
We want to test out this nf-core workflow: https://github.com/nf-core/differentialabundance for our RNAseq data output.
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