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1. C.briggsae-C.nigoni-Viswanath-Cutter-2023 C.briggsae-C.nigoni-Viswanath-Cutter-2023 Public

   This repository contains the code and data needed to replicate the analyses, results, and figures from Viswanath & Cutter (2023).

   Shell

2. Evolution-of-expression-plasticity-Caenorhabditis Evolution-of-expression-plasticity-Caenorhabditis Public

   On-going analysis for C. remanei and C. latens datasets. This dataset contains data for two species (C. remanei & C. latens), sex (males & females) and tissues (gonad & soma)

   R

3. Viswanath-Cutter-2024_Paper2 Viswanath-Cutter-2024_Paper2 Public

   On-going analysis for C. remanei and C. latens datasets focused on regulatory divergence and hybrid incompatibility

   R

4. Local-PCA-to-identify-structural-variation- Local-PCA-to-identify-structural-variation- Public

   Windows-compatible Local PCA pipeline to detect structural variants and polymorphic regions in wild house mice. Includes custom VCF processing, outlier detection via PCA, interactive RShiny inspect…

   R

5. TE-associated-Gene-expression-Analysis TE-associated-Gene-expression-Analysis Public

   on-going analysis to understand the effects of potential adaptive Transposable elements on gene expression in house mice

6. All_Methods_Notes All_Methods_Notes Public

   This is to create a repository of different methods/stats I have used/come across for reference. Each method will have sections for purpose, inputs, outputs, how it works, example code (where relev…