AWK(1) •
AcerCCC(3) •
Alignment(1) •
Basespace(3) •
Bash(10) •
Bowtie(1) •
Budgeting(1) •
CCC(2) •
Ch2(1) •
Ch2 Temp Variability(10) •
Ch3(1) •
Ch3 Reciprocal Transplant(3) •
Ch4 AcerCCC(23) •
Coding(57) •
Cutadapt(3) •
DESeq2(3) •
De Novo Transcriptome(1) •
De Novo Transcriptome Assembly(2) •
FastQC(3) •
Fish Predation(1) •
Fisher Exact Test(3) •
GLMM(3) •
GO Enrichment(6) •
Git(1) •
GitHub(1) •
IPAM(2) •
Kevin(6) •
Linear Mixed Models(3) •
MDS(1) •
Michael(2) •
MultiQC(2) •
NCBI(1) •
Natalia(1) •
PAM(3) •
PCA(2) •
PCoA(1) •
PERMANOVA(2) •
PSTR(1) •
Parallel(1) •
Pegasus(14) •
Pocillopora damicornis(2) •
Pseudodiploria strigosa(1) •
R(11) •
RNA(1) •
RNA Seq(3) •
RNAseq(1) •
Reciprocal Transplant(4) •
SRA(1) •
STAR(1) •
Sequencing(5) •
SortMeRNA(1) •
Statistics(2) •
Stats(1) •
Stress Hardening(8) •
Temperature Variability 2023(11) •
TopGO(4) •
Transcriptomics(11) •
Trim Galore(2) •
Trimmomatic(1) •
Trinity(1) •
Venn Diagrams(1) •
WGCNA(2) •
Wound Healing(12) •
glmmTMB(2) •
rRNA(2) •
reciprocaltransplant(1) •
trimming(1)
AWK 1
- creating .txt file with just sample names using awk/sed • June 3, 2023
AcerCCC 3
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
- notes on alignment tools • June 14, 2023
- some wins against Pegasus • June 7, 2023
Alignment 1
- notes on alignment tools • June 14, 2023
Basespace 3
- Downloading sequences from Basespace and uploading sequences to NCBI • October 18, 2024
- Downloading stress-hardening sequences from BaseSpace • May 15, 2023
- Optimizing command line on new laptop for bash scripts for downloading raw sequences • May 4, 2023
Bash 10
- Optimizing command line on new laptop for bash scripts for downloading raw sequences • May 4, 2023
- Revisiting Pegasus (UM Supercomputer) after 4 years • May 24, 2023
- Uploading files to Pegasus • May 31, 2023
- creating .txt file with just sample names using awk/sed • June 3, 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
- some wins against Pegasus • June 7, 2023
- writing a script to create multiple jobs at once for trimming • June 3, 2023
Bowtie 1
- notes on alignment tools • June 14, 2023
Budgeting 1
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
CCC 2
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- Uploading files to Pegasus • May 31, 2023
Ch2 1
- 2024-02-12-noteaboutannotationfilesfromMS.md • February 12, 2024
Ch2 Temp Variability 10
- Addressing reviewer comments for stress-hardening paper • July 1, 2025
- Ch2 Acer DESeq2 • August 14, 2023
- HISAT2 alignment • July 23, 2023
- Pcli Salmon transcriptome • July 26, 2023
- STAR index and alignment for Pcli • July 25, 2023
- Tximport for salmon quant Pcli • August 3, 2023
- pre-filtering samples based on million reads • August 16, 2023
- redo Fastp for Ch2 samples • August 8, 2023
- stringtie2 for Ch2 temp variability • July 25, 2023
- using Pcli transcriptome • July 25, 2023
Ch3 1
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
Ch3 Reciprocal Transplant 3
- Fish Predation GLMMs • October 25, 2025
- Using SortmeRNA • September 22, 2025
- denovo Transcriptome Assembly for Pstr • July 25, 2025
Ch4 AcerCCC 23
- Acer CCC KEGG Pathway analysis issues • April 27, 2024
- Acer CCC versus Acer Stress-Hardening Samples • July 6, 2023
- Acer genomes vs transcriptomes • June 15, 2023
- Aligning raw reads versus trimmed reads results for Acer CCC samples • June 26, 2023
- Ch4_AcerCCC read counts • August 20, 2023
- Ch4_AcerCCC updated gff STAR alignment results • July 21, 2023
- DESeq2 for Ch4 CCC samples (both location and genotype in dds model) • July 28, 2023
- STAR align updated to counts matrix • July 21, 2023
- STAR alignment troubleshooting • June 21, 2023
- STAR index Acer genome • June 21, 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
- Take 2 with CRW DHW MMM • March 21, 2024
- Troubleshooting STAR alignment • July 3, 2023
- Which samples to use based on minimum library size • June 15, 2023
- initial attempt STAR alignment codes • June 15, 2023
- interpreting STAR alignment output files • June 26, 2023
- md5 check sums script • July 19, 2023
- samtools for STAR alignment results • June 27, 2023
- stringtie code for Acer CCC and rerunning STAR with updated annotation file • June 27, 2023
- updated stringtie code • July 22, 2023
Coding 57
- 2024-02-12-noteaboutannotationfilesfromMS.md • February 12, 2024
- Acer CCC KEGG Pathway analysis issues • April 27, 2024
- 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
- Addressing reviewer comments for stress-hardening paper • July 1, 2025
- 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
- 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
- Fv/Fm GLMMs • December 23, 2023
- HISAT2 alignment • July 23, 2023
- Issue with FvFm code • December 24, 2023
- Libro et al. 2013 Acer genome alignment attempt • November 24, 2023
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
- 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
- Take 2 with CRW DHW MMM • March 21, 2024
- 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
- Using gitignore file for GitHub public repository • April 10, 2025
- Which samples to use based on minimum library size • June 15, 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
- 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
Cutadapt 3
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
- Trimmomatic vs. Cutadapt • June 3, 2023
- installing cutadapt and trim_galore on Pegasus • June 2, 2023
DESeq2 3
- Addressing reviewer comments for stress-hardening paper • July 1, 2025
- DEGPatterns Gene Clustering • November 22, 2022
- PCA plot significance • November 21, 2022
De Novo Transcriptome 1
- denovo Transcriptome Assembly for Pstr • July 25, 2025
De Novo Transcriptome Assembly 2
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
FastQC 3
- Helpful articles for quality control and pre-processing of RNA-seq data • June 5, 2023
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
Fish Predation 1
- Fish Predation GLMMs • October 25, 2025
Fisher Exact Test 3
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- topGO Analysis • November 15, 2022
GLMM 3
- Fish Predation GLMMs • October 25, 2025
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
GO Enrichment 6
- Adding gene lists to GO tables • May 8, 2023
- GO Analysis • November 22, 2022
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- Separating Up- and Down-Regulated Genes for GO Analysis? • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- topGO Analysis • November 15, 2022
Git 1
- Using gitignore file for GitHub public repository • April 10, 2025
GitHub 1
- Using gitignore file for GitHub public repository • April 10, 2025
IPAM 2
- Fv/Fm GLMMs • December 23, 2023
- Issue with FvFm code • December 24, 2023
Kevin 6
- 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
- PCA plot significance • November 21, 2022
- Separating Up- and Down-Regulated Genes for GO Analysis? • February 8, 2023
- notes on alignment tools • June 14, 2023
Linear Mixed Models 3
- 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
MDS 1
- Creating Polygons for PCAs • February 8, 2023
Michael 2
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- notes on alignment tools • June 14, 2023
MultiQC 2
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
- installing MultiQC on pegasus • June 1, 2023
NCBI 1
- Downloading sequences from Basespace and uploading sequences to NCBI • October 18, 2024
Natalia 1
- notes on alignment tools • June 14, 2023
PAM 3
- Figuring out why R code for importing PAM data stopped working • January 21, 2023
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
PCA 2
- Creating Polygons for PCAs • February 8, 2023
- PCA plot significance • November 21, 2022
PCoA 1
- Addressing reviewer comments for stress-hardening paper • July 1, 2025
PERMANOVA 2
- Creating Polygons for PCAs • February 8, 2023
- PCA plot significance • November 21, 2022
PSTR 1
- Using SortmeRNA • September 22, 2025
Parallel 1
Pegasus 14
- Downloading sequences from Box • March 7, 2025
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
- Revisiting Pegasus (UM Supercomputer) after 4 years • May 24, 2023
- Uploading files to Pegasus • May 31, 2023
- Using SortmeRNA • September 22, 2025
- 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
- some wins against Pegasus • June 7, 2023
- writing a script to create multiple jobs at once for trimming • June 3, 2023
Pocillopora damicornis 2
- GO Analysis • November 22, 2022
- topGO Analysis • November 15, 2022
Pseudodiploria strigosa 1
- denovo Transcriptome Assembly for Pstr • July 25, 2025
R 11
- Adding gene lists to GO tables • May 8, 2023
- Creating Polygons for PCAs • February 8, 2023
- DEGPatterns Gene Clustering • November 22, 2022
- Figuring out why R code for importing PAM data stopped working • January 21, 2023
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- GO Analysis • November 22, 2022
- PCA plot significance • November 21, 2022
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- Venn Diagrams • November 22, 2022
- topGO Analysis • November 15, 2022
RNA 1
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
RNA Seq 3
- Helpful articles for quality control and pre-processing of RNA-seq data • June 5, 2023
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- Trimmomatic vs. Cutadapt • June 3, 2023
RNAseq 1
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
Reciprocal Transplant 4
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- Using SortmeRNA • September 22, 2025
SRA 1
- Downloading sequences from Basespace and uploading sequences to NCBI • October 18, 2024
STAR 1
- notes on alignment tools • June 14, 2023
Sequencing 5
- 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
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
SortMeRNA 1
- Using SortmeRNA • September 22, 2025
Statistics 2
- Figuring out Linear Mixed Models using Stress-Hardening Data • January 10, 2023
- topGO Analysis • November 15, 2022
Stats 1
- Notes on GLMs • August 20, 2024
Stress Hardening 8
- Figuring out Linear Mixed Models using Stress-Hardening Data • January 10, 2023
- Figuring out why R code for importing PAM data stopped working • January 21, 2023
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
- notes on alignment tools • June 14, 2023
- some wins against Pegasus • June 7, 2023
Temperature Variability 2023 11
- Acer CCC versus Acer Stress-Hardening Samples • July 6, 2023
- Acer genomes vs transcriptomes • June 15, 2023
- STAR alignment troubleshooting • June 21, 2023
- STAR index Acer genome • June 21, 2023
- SUCCESS STAR alignment Acer genome • June 21, 2023
- Starting over • July 18, 2023
- Which samples to use based on minimum library size • June 15, 2023
- download fastp to Pegasus and running fastp • July 19, 2023
- initial attempt STAR alignment codes • June 15, 2023
- md5 check sums script • July 19, 2023
- stringtie on SH samples • July 5, 2023
TopGO 4
- GO Analysis • November 22, 2022
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- topGO Analysis • November 15, 2022
Transcriptomics 11
- Adding gene lists to GO tables • May 8, 2023
- Creating Polygons for PCAs • February 8, 2023
- DEGPatterns Gene Clustering • November 22, 2022
- GO Analysis • November 22, 2022
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 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
- Venn Diagrams • November 22, 2022
- topGO Analysis • November 15, 2022
Trim Galore 2
- installing cutadapt and trim_galore on Pegasus • June 2, 2023
- writing a script to create multiple jobs at once for trimming • June 3, 2023
Trimmomatic 1
- Trimmomatic vs. Cutadapt • June 3, 2023
Trinity 1
- denovo Transcriptome Assembly for Pstr • July 25, 2025
Venn Diagrams 1
- Venn Diagrams • November 22, 2022
WGCNA 2
- WGCNA for wound healing manuscript • June 6, 2023
- WGCNA for wound healing manuscript pt. 2 • June 7, 2023
Wound Healing 12
- Adding gene lists to GO tables • May 8, 2023
- Creating Polygons for PCAs • February 8, 2023
- DEGPatterns Gene Clustering • November 22, 2022
- GO Analysis • November 22, 2022
- PCA plot significance • November 21, 2022
- Re-running TopGO with Up vs. Downregulated genes split up • February 8, 2023
- TopGO = what does it all mean????? • February 8, 2023
- Venn Diagrams • November 22, 2022
- WGCNA for wound healing manuscript • June 6, 2023
- WGCNA for wound healing manuscript pt. 2 • June 7, 2023
- notes on alignment tools • June 14, 2023
- topGO Analysis • November 15, 2022
glmmTMB 2
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
rRNA 2
- Next steps with PSTR RT transcriptomics • January 8, 2026
- Notes on Pstrigosa bioinformatics data analysis • August 20, 2025
reciprocaltransplant 1
- Redoing trimming of reciprocal transplant seqs • August 4, 2025
trimming 1
- Redoing trimming of reciprocal transplant seqs • August 4, 2025