| Date | Title | Categories |
|---|---|---|
| Jan 8, 2026 | Next steps with PSTR RT transcriptomics | Analysis, Reciprocal Transplant, Coding, Pegasus, rRNA, De Novo Transcriptome Assembly |
| Oct 25, 2025 | Fish Predation GLMMs | Analysis, Processing, Fish Predation, Reciprocal Transplant, GLMM |
| Sep 22, 2025 | Using SortmeRNA | Analysis, Processing, Reciprocal Transplant, PSTR, SortMeRNA, Pegasus |
| Aug 20, 2025 | Notes on Pstrigosa bioinformatics data analysis | Analysis, Reciprocal Transplant, Coding, Pegasus, rRNA, De Novo Transcriptome Assembly |
| Aug 4, 2025 | Redoing trimming of reciprocal transplant seqs | Analysis, Processing, Reciprocal Transplant, RNA-Seq, Trimming, Cutadapt, Pegasus |
| Jul 25, 2025 | denovo Transcriptome Assembly for Pstr | Analysis, Processing, De Novo Transcriptome Assembly, Trinity, Pseudodiploria strigosa, Reciprocal Transplant |
| Jul 1, 2025 | Addressing reviewer comments for stress-hardening paper | Analysis, Coding, Ch2 Temp Variability, Stress-Hardening, DESeq2, PCoA |
| Apr 10, 2025 | Using gitignore file for GitHub public repository | Processing, Coding, Git, GitHub |
| Mar 7, 2025 | Downloading sequences from Box | Bioinformatics, Pegasus |
| Oct 18, 2024 | Downloading sequences from Basespace and uploading sequences to NCBI | Bioinformatics, Basespace, NCBI, SRA |
| Aug 20, 2024 | Notes on GLMs | Stats |
| Apr 27, 2024 | Acer CCC KEGG Pathway analysis issues | Analysis, Processing, Ch4 AcerCCC, Coding |
| Mar 21, 2024 | Take 2 with CRW DHW MMM | Analysis, Processing, Ch4 AcerCCC, Coding |
| Feb 12, 2024 | 2024-02-12-noteaboutannotationfilesfromMS.md | Analysis, Ch2 Temp Variability, Stress-Hardening, Coding |
| Dec 24, 2023 | Issue with FvFm code | Coding, IPAM |
| Dec 23, 2023 | Fv/Fm GLMMs | Coding, IPAM |
| Dec 18, 2023 | installing and using reefmapmaker to create coral reef maps | Coding |
| Dec 7, 2023 | Annotating new Acer transcriptome | Coding |
| Dec 7, 2023 | Acer gene counts using samtools | Coding |
| Dec 4, 2023 | Downloading SST Data from CoralWatch | Coding |
| Nov 28, 2023 | UTR gff parser | Coding |
| Nov 24, 2023 | Libro et al. 2013 Acer genome alignment attempt | Coding |
| Nov 22, 2023 | new Acer genome continued | Coding |
| Nov 17, 2023 | Conda Environment on Pegasus, new Acer genome, and bowtie2 | Coding |
| Nov 6, 2023 | Trouble with Fv/Fm Data | Coding |
| Aug 23, 2023 | DESeq2 design formula | Coding |
| Aug 21, 2023 | PCR duplicates | Coding |
| Aug 20, 2023 | Ch4_AcerCCC read counts | Coding, Ch4 AcerCCC |
| Aug 16, 2023 | pre-filtering samples based on million reads | Coding, Ch2 Temp Variability, Stress-Hardening |
| Aug 14, 2023 | Ch2 Acer DESeq2 | Coding, Ch2 Temp Variability, Stress-Hardening |
| Aug 8, 2023 | redo Fastp for Ch2 samples | Coding, Ch2 Temp Variability, Stress-Hardening |
| Aug 3, 2023 | Tximport for salmon quant Pcli | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 28, 2023 | DESeq2 for Ch4 CCC samples (both location and genotype in dds model) | Coding, Ch4 AcerCCC |
| Jul 26, 2023 | Pcli Salmon transcriptome | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 25, 2023 | using Pcli transcriptome | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 25, 2023 | stringtie2 for Ch2 temp variability | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 25, 2023 | STAR index and alignment for Pcli | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 23, 2023 | HISAT2 alignment | Coding, Ch2 Temp Variability, Stress-Hardening |
| Jul 23, 2023 | renaming trimmed files | Coding |
| Jul 22, 2023 | updated stringtie code | Coding, Ch4 AcerCCC |
| Jul 21, 2023 | STAR align updated to counts matrix | Coding, Ch4 AcerCCC |
| Jul 21, 2023 | troubleshooting STAR index (again) | Coding |
| Jul 21, 2023 | Ch4_AcerCCC updated gff STAR alignment results | Coding, Ch4 AcerCCC |
| Jul 21, 2023 | Pcli transcriptome | Coding |
| Jul 19, 2023 | download fastp to Pegasus and running fastp | Coding, Stress-Hardening |
| Jul 19, 2023 | md5 check sums script | Coding, Stress-Hardening, Ch4 AcerCCC |
| Jul 18, 2023 | Starting over | Coding, Stress-Hardening, Ch4 AcerCCC |
| Jul 6, 2023 | Acer CCC versus Acer Stress-Hardening Samples | Coding, Stress-Hardening, Ch4 AcerCCC |
| Jul 5, 2023 | Subread and FeatureCounts | Coding, Ch4 AcerCCC |
| Jul 5, 2023 | stringtie on SH samples | Coding, Stress-Hardening |
| Jul 3, 2023 | Troubleshooting STAR alignment | Coding, Ch4 AcerCCC |
| Jun 29, 2023 | STAR output to gene counts | Coding, Ch4 AcerCCC |
| Jun 27, 2023 | following HBC pipeline - qualimap and salmon | Coding |
| Jun 27, 2023 | samtools for STAR alignment results | Coding, Ch4 AcerCCC |
| Jun 27, 2023 | stringtie code for Acer CCC and rerunning STAR with updated annotation file | Coding, Ch4 AcerCCC |
| Jun 26, 2023 | Aligning raw reads versus trimmed reads results for Acer CCC samples | Coding, Ch4 AcerCCC |
| Jun 26, 2023 | interpreting STAR alignment output files | Coding, Ch4 AcerCCC |
| Jun 24, 2023 | stringtie articles | Coding |
| Jun 21, 2023 | SUCCESS STAR alignment Acer genome | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 21, 2023 | STAR alignment troubleshooting | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 21, 2023 | STAR index Acer genome | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 15, 2023 | Which samples to use based on minimum library size | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 15, 2023 | initial attempt STAR alignment codes | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 15, 2023 | Acer genomes vs transcriptomes | Coding, Ch4 AcerCCC, Stress-Hardening |
| Jun 14, 2023 | notes on alignment tools | Bioinformatics, STAR, Bowtie, Michael, Natalia, Wound Healing, Ch4 AcerCCC, Stress-Hardening, Kevin, Alignment, Bash, Pegasus |
| Jun 7, 2023 | some wins against Pegasus | Coding, Pegasus, Bash, Stress-Hardening, Ch4 AcerCCC |
| Jun 7, 2023 | WGCNA for wound healing manuscript pt. 2 | Bioinformatics, WGCNA, Wound Healing |
| Jun 6, 2023 | WGCNA for wound healing manuscript | Bioinformatics, WGCNA, Wound Healing |
| Jun 5, 2023 | Helpful articles for quality control and pre-processing of RNA-seq data | Bioinformatics, FastQC, Sequencing, RNA-Seq |
| Jun 3, 2023 | creating .txt file with just sample names using awk/sed | Coding, Bash, AWK |
| Jun 3, 2023 | writing a script to create multiple jobs at once for trimming | Coding, Bioinformatics, Pegasus, Bash, Parallel, Trim Galore |
| Jun 3, 2023 | Trimmomatic vs. Cutadapt | Bioinformatics, Trimmomatic, Cutadapt, RNA-Seq |
| Jun 2, 2023 | installing cutadapt and trim_galore on Pegasus | Bioinformatics, Cutadapt, Trim Galore, Pegasus, Bash |
| Jun 1, 2023 | initial FastQC results for Acer CCC samples (untrimmed) | Bioinformatics, Dissertation, Pegasus, FastQC, Ch4 AcerCCC, Bash, Sequencing, MultiQC |
| Jun 1, 2023 | installing MultiQC on pegasus | Bioinformatics, Pegasus, MultiQC, Bash |
| May 31, 2023 | Uploading files to Pegasus | Bioinformatics, Pegasus, Bash, Ch4 AcerCCC |
| May 24, 2023 | Revisiting Pegasus (UM Supercomputer) after 4 years | Bioinformatics, Pegasus, Transcriptomics, Bash |
| May 24, 2023 | QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment | Bioinformatics, Dissertation, Stress-Hardening, Transcriptomics, Pegasus, FastQC, Ch4 AcerCCC |
| May 15, 2023 | Downloading stress-hardening sequences from BaseSpace | Bioinformatics, Sequencing, Basespace |
| May 8, 2023 | Adding gene lists to GO tables | Bioinformatics, Wound Healing, R, Transcriptomics, GO Enrichment |
| May 4, 2023 | Optimizing command line on new laptop for bash scripts for downloading raw sequences | Bioinformatics, Bash, Basespace, Sequencing |
| Feb 8, 2023 | Separating Up- and Down-Regulated Genes for GO Analysis? | Bioinformatics, GO Enrichment, Transcriptomics, Kevin |
| Feb 8, 2023 | Re-running TopGO with Up vs. Downregulated genes split up | Bioinformatics, TopGO, R, Wound Healing, Transcriptomics, Fisher Exact Test, GO Enrichment |
| Feb 8, 2023 | Creating Polygons for PCAs | Coding, PCA, R, Wound Healing, Transcriptomics, MDS, PERMANOVA |
| Feb 8, 2023 | TopGO = what does it all mean????? | Bioinformatics, TopGO, R, GO Enrichment, Wound Healing, Transcriptomics, Fisher Exact Test |
| Jan 31, 2023 | More notes on GLMMs (with Dr. Kevin Wong!) | Coding, Stats, GLMM, Linear Mixed Models, PAM, Stress-Hardening, glmmTMB, Kevin |
| Jan 29, 2023 | GLMMS for Stress-Hardening IPAM Data | Coding, Stats, GLMM, Linear Mixed Models, PAM, Stress-Hardening, glmmTMB, R, Kevin |
| Jan 21, 2023 | Figuring out why R code for importing PAM data stopped working | Coding, R, PAM, Stress-Hardening |
| Jan 10, 2023 | Figuring out Linear Mixed Models using Stress-Hardening Data | Stats, Linear Mixed Models, Stress-Hardening, Kevin |
| Nov 22, 2022 | DEGPatterns Gene Clustering | Coding, DESeq2, Wound Healing, Transcriptomics, R |
| Nov 22, 2022 | GO Analysis | Coding, Transcriptomics, Wound Healing, Pocillopora damicornis, TopGO, R, GO Enrichment |
| Nov 22, 2022 | Venn Diagrams | Coding, Wound Healing, Transcriptomics, R, Venn Diagrams |
| Nov 21, 2022 | PCA plot significance | Coding, R, PCA, Wound Healing, DESeq2, PERMANOVA, Kevin |
| Nov 15, 2022 | topGO Analysis | Stats, Transcriptomics, Wound Healing, Pocillopora damicornis, TopGO, R, GO Enrichment, Fisher Exact Test |
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