Pinned Repositories
aiptasia_multi-omics
Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts!
anna_karenina
Scripts used in the paper "Long-Term Temperature Stress in the Coral Model Aiptasia Supports the 'Anna Karenina Principle' for Bacterial Microbiomes"
annotating_proteomes
How to annotate protein gene models (e.g. for genome projects)--not just textual annotation of probable gene function, but also with GO terms.
bismsmark
Uses `snakemake` to run `bismark` in a reproducible pipeline. Can be run locally, or on a cluster running the SLURM scheduler.
common
Scripts to automate myself out of a job!
cpgberus
Benchmarking different ways to assay methylation levels.
pdae_dna_meth
Scripts and important data for the manuscript "Intergenerational epigenetic inheritance in reef-building corals"
spis_dna_meth
Scripts used to analyse the epigenetic response of the coral S. pistillata to pH stress.
topGO_pipeline
How to perform GO term enrichment analysis using topGO (Alexa et al., 2006).
working_with_dna_meth
Pipeline that I use to process DNA methylation data--both theory and implementation included!
lyijin's Repositories
lyijin/topGO_pipeline
How to perform GO term enrichment analysis using topGO (Alexa et al., 2006).
lyijin/working_with_dna_meth
Pipeline that I use to process DNA methylation data--both theory and implementation included!
lyijin/annotating_proteomes
How to annotate protein gene models (e.g. for genome projects)--not just textual annotation of probable gene function, but also with GO terms.
lyijin/pdae_dna_meth
Scripts and important data for the manuscript "Intergenerational epigenetic inheritance in reef-building corals"
lyijin/bismsmark
Uses `snakemake` to run `bismark` in a reproducible pipeline. Can be run locally, or on a cluster running the SLURM scheduler.
lyijin/common
Scripts to automate myself out of a job!
lyijin/cpgberus
Benchmarking different ways to assay methylation levels.
lyijin/aiptasia_multi-omics
Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts!
lyijin/anna_karenina
Scripts used in the paper "Long-Term Temperature Stress in the Coral Model Aiptasia Supports the 'Anna Karenina Principle' for Bacterial Microbiomes"
lyijin/spis_dna_meth
Scripts used to analyse the epigenetic response of the coral S. pistillata to pH stress.
lyijin/email_analysis
When one gets bored during Christmas and has 3+ years of email data to play around with...
lyijin/exaiptasia_datasheet
Repository containing code and datasheet to generate datasheet for the Exaiptasia multi-omics experiment.
lyijin/increased_incompatibility
Code and intermediate files to replicate analysis for a manuscript in review.
lyijin/lyijin.github.io
Repo for the HTML/CSS code for my personal website
lyijin/notes_for_future_me
Stuff that I find useful--but I don't use often enough to commit to my (aging) memory
lyijin/pdae_parental_genotypes
Key scripts and intermediate files to call Platygyra daedalea parental genotypes
lyijin/smic_dna_meth
The role of DNA methylation in the dinoflagellate coral symbiont Symbiodinium microadriaticum
lyijin/teaching_slides
Slides for teaching
lyijin/twital
Script & instructions to automate generation of lab weekly newsletter.