Analysis(10) •
Bioinformatics(21) •
Budgeting(1) •
Coding(61) •
Dissertation(3) •
Processing(7) •
Stats(5)
Analysis 10
- 2024-02-12-noteaboutannotationfilesfromMS.md • February 12, 2024
- Acer CCC KEGG Pathway analysis issues • April 27, 2024
- Addressing reviewer comments for stress-hardening paper • July 1, 2025
- Fish Predation GLMMs • October 25, 2025
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
- Take 2 with CRW DHW MMM • March 21, 2024
- Using SortmeRNA • September 22, 2025
- denovo Transcriptome Assembly for Pstr • July 25, 2025
Bioinformatics 21
- Adding gene lists to GO tables • May 8, 2023
- Downloading sequences from Basespace and uploading sequences to NCBI • October 18, 2024
- Downloading sequences from Box • March 7, 2025
- Downloading stress-hardening sequences from BaseSpace • May 15, 2023
- Helpful articles for quality control and pre-processing of RNA-seq data • June 5, 2023
- Optimizing command line on new laptop for bash scripts for downloading raw sequences • May 4, 2023
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- Revisiting Pegasus (UM Supercomputer) after 4 years • May 24, 2023
- Separating Up- and Down-Regulated Genes for GO Analysis? • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- Trimmomatic vs. Cutadapt • June 3, 2023
- Uploading files to Pegasus • May 31, 2023
- WGCNA for wound healing manuscript • June 6, 2023
- WGCNA for wound healing manuscript pt. 2 • June 7, 2023
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
- installing MultiQC on pegasus • June 1, 2023
- installing cutadapt and trim_galore on Pegasus • June 2, 2023
- notes on alignment tools • June 14, 2023
- writing a script to create multiple jobs at once for trimming • June 3, 2023
Budgeting 1
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
Coding 61
- Acer CCC versus Acer Stress-Hardening Samples • July 6, 2023
- Acer gene counts using samtools • December 7, 2023
- Acer genomes vs transcriptomes • June 15, 2023
- Aligning raw reads versus trimmed reads results for Acer CCC samples • June 26, 2023
- Annotating new Acer transcriptome • December 7, 2023
- Ch2 Acer DESeq2 • August 14, 2023
- Ch4_AcerCCC read counts • August 20, 2023
- Ch4_AcerCCC updated gff STAR alignment results • July 21, 2023
- Conda Environment on Pegasus, new Acer genome, and bowtie2 • November 17, 2023
- Creating Polygons for PCAs • February 8, 2023
- DEGPatterns Gene Clustering • November 22, 2022
- DESeq2 design formula • August 23, 2023
- DESeq2 for Ch4 CCC samples (both location and genotype in dds model) • July 28, 2023
- Downloading SST Data from CoralWatch • December 4, 2023
- Figuring out why R code for importing PAM data stopped working • January 21, 2023
- Fv/Fm GLMMs • December 23, 2023
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- GO Analysis • November 22, 2022
- HISAT2 alignment • July 23, 2023
- Issue with FvFm code • December 24, 2023
- Libro et al. 2013 Acer genome alignment attempt • November 24, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
- PCA plot significance • November 21, 2022
- PCR duplicates • August 21, 2023
- Pcli Salmon transcriptome • July 26, 2023
- Pcli transcriptome • July 21, 2023
- STAR align updated to counts matrix • July 21, 2023
- STAR alignment troubleshooting • June 21, 2023
- STAR index Acer genome • June 21, 2023
- STAR index and alignment for Pcli • July 25, 2023
- STAR output to gene counts • June 29, 2023
- SUCCESS STAR alignment Acer genome • June 21, 2023
- Starting over • July 18, 2023
- Subread and FeatureCounts • July 5, 2023
- Trouble with Fv/Fm Data • November 6, 2023
- Troubleshooting STAR alignment • July 3, 2023
- Tximport for salmon quant Pcli • August 3, 2023
- UTR gff parser • November 28, 2023
- Venn Diagrams • November 22, 2022
- Which samples to use based on minimum library size • June 15, 2023
- creating .txt file with just sample names using awk/sed • June 3, 2023
- download fastp to Pegasus and running fastp • July 19, 2023
- following HBC pipeline - qualimap and salmon • June 27, 2023
- initial attempt STAR alignment codes • June 15, 2023
- installing and using reefmapmaker to create coral reef maps • December 18, 2023
- interpreting STAR alignment output files • June 26, 2023
- md5 check sums script • July 19, 2023
- new Acer genome continued • November 22, 2023
- pre-filtering samples based on million reads • August 16, 2023
- redo Fastp for Ch2 samples • August 8, 2023
- renaming trimmed files • July 23, 2023
- samtools for STAR alignment results • June 27, 2023
- some wins against Pegasus • June 7, 2023
- stringtie articles • June 24, 2023
- stringtie code for Acer CCC and rerunning STAR with updated annotation file • June 27, 2023
- stringtie on SH samples • July 5, 2023
- stringtie2 for Ch2 temp variability • July 25, 2023
- troubleshooting STAR index (again) • July 21, 2023
- updated stringtie code • July 22, 2023
- using Pcli transcriptome • July 25, 2023
- writing a script to create multiple jobs at once for trimming • June 3, 2023
Dissertation 3
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
Processing 7
- Acer CCC KEGG Pathway analysis issues • April 27, 2024
- Fish Predation GLMMs • October 25, 2025
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
- Take 2 with CRW DHW MMM • March 21, 2024
- Using SortmeRNA • September 22, 2025
- Using gitignore file for GitHub public repository • April 10, 2025
- denovo Transcriptome Assembly for Pstr • July 25, 2025
Stats 5
- Figuring out Linear Mixed Models using Stress-Hardening Data • January 10, 2023
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
- Notes on GLMs • August 20, 2024
- topGO Analysis • November 15, 2022