AcerCCC(3) •
Basespace(3) •
Bowtie(1) •
Budgeting(1) •
CCC(2) •
CCC_ch4(17) •
Ch2(1) •
Ch2_tempvariability(5) •
Ch4_AcerCCC(5) •
Coding(11) •
DESeq2(2) •
FastQC(3) •
Fisher Exact Test(3) •
GLMM(2) •
GO Enrichment(6) •
IPAM(2) •
Kevin(6) •
Linear Mixed Models(3) •
MDS(1) •
Michael(2) •
NCBI(1) •
Natalia(1) •
PAM(3) •
PCA(2) •
PERMANOVA(2) •
Pegasus(9) •
Pocillopora damicornis(2) •
R(11) •
RNA(1) •
RNA Seq(2) •
RNA seq(1) •
Reciprocal Transplant(1) •
SRA(1) •
STAR(1) •
Sequencing(5) •
Statistics(2) •
Stress Hardening(6) •
Transcriptomics(11) •
Trimmomatic(1) •
WGCNA(2) •
alignment(1) •
awk(1) •
bash(10) •
ch2_tempvariability(4) •
ch4_CCC(1) •
coding(42) •
cutadapt(2) •
glmmTMB(2) •
multiqc(2) •
parallel(1) •
stats(1) •
stress hardening(2) •
temperaturevariability2023(11) •
topGO(4) •
trim_galore(2) •
venn diagrams(1) •
wound healing(12)
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
Basespace 3
- Downloading sequences from Basespace • 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
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
CCC_ch4 17
- 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
- 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
- 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
Ch2 1
- 2024-02-12-noteaboutannotationfilesfromMS.md • February 12, 2024
Ch2_tempvariability 5
- HISAT2 alignment • July 23, 2023
- Pcli Salmon transcriptome • July 26, 2023
- STAR index and alignment for Pcli • July 25, 2023
- stringtie2 for Ch2 temp variability • July 25, 2023
- using Pcli transcriptome • July 25, 2023
Ch4_AcerCCC 5
- Acer CCC KEGG Pathway analysis issues • April 27, 2024
- Ch4_AcerCCC read counts • August 20, 2023
- Ch4_AcerCCC updated gff STAR alignment results • July 21, 2023
- Take 2 with CRW DHW MMM • March 21, 2024
- updated stringtie code • July 22, 2023
Coding 11
- Acer gene counts using samtools • December 7, 2023
- Annotating new Acer transcriptome • December 7, 2023
- Conda Environment on Pegasus, new Acer genome, and bowtie2 • November 17, 2023
- Downloading SST Data from CoralWatch • December 4, 2023
- Fv/Fm GLMMs • December 23, 2023
- Issue with FvFm code • December 24, 2023
- Libro et al. 2013 Acer genome alignment attempt • November 24, 2023
- Trouble with Fv/Fm Data • November 6, 2023
- UTR gff parser • November 28, 2023
- installing and using reefmapmaker to create coral reef maps • December 18, 2023
- new Acer genome continued • November 22, 2023
DESeq2 2
- DEGPatterns Gene Clustering • November 22, 2022
- PCA plot significance • November 21, 2022
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
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 2
- 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
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
NCBI 1
- Downloading sequences from Basespace • 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
PERMANOVA 2
- Creating Polygons for PCAs • February 8, 2023
- PCA plot significance • November 21, 2022
Pegasus 9
- QC scripts for Pegasus Stress-Hardening RNA-Seq Experiment • May 24, 2023
- Revisiting Pegasus (UM Supercomputer) after 4 years • May 24, 2023
- Uploading files to Pegasus • May 31, 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
Pocillopora damicornis 2
- GO Analysis • November 22, 2022
- topGO Analysis • November 15, 2022
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 2
- 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
RNA seq 1
- Trimmomatic vs. Cutadapt • June 3, 2023
Reciprocal Transplant 1
- RNA Sequencing Contract with Dr. Michael Studivan • February 8, 2023
SRA 1
- Downloading sequences from Basespace • 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
Statistics 2
- Figuring out Linear Mixed Models using Stress-Hardening Data • January 10, 2023
- topGO Analysis • November 15, 2022
Stress Hardening 6
- 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
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
Trimmomatic 1
- Trimmomatic vs. Cutadapt • June 3, 2023
WGCNA 2
- WGCNA for wound healing manuscript • June 6, 2023
- WGCNA for wound healing manuscript pt. 2 • June 7, 2023
alignment 1
- notes on alignment tools • June 14, 2023
awk 1
- creating .txt file with just sample names using awk/sed • June 3, 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
ch2_tempvariability 4
- Ch2 Acer DESeq2 • August 14, 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
ch4_CCC 1
coding 42
- 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 genomes vs transcriptomes • June 15, 2023
- Aligning raw reads versus trimmed reads results for Acer CCC samples • June 26, 2023
- Ch2 Acer DESeq2 • August 14, 2023
- Ch4_AcerCCC read counts • August 20, 2023
- Ch4_AcerCCC updated gff STAR alignment results • July 21, 2023
- DESeq2 design formula • August 23, 2023
- DESeq2 for Ch4 CCC samples (both location and genotype in dds model) • July 28, 2023
- HISAT2 alignment • July 23, 2023
- 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
- Troubleshooting STAR alignment • July 3, 2023
- Tximport for salmon quant Pcli • August 3, 2023
- 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
- interpreting STAR alignment output files • June 26, 2023
- md5 check sums script • July 19, 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 2
- Trimmomatic vs. Cutadapt • June 3, 2023
- installing cutadapt and trim_galore on Pegasus • June 2, 2023
glmmTMB 2
- GLMMS for Stress-Hardening IPAM Data • January 29, 2023
- More notes on GLMMs (with Dr. Kevin Wong!) • January 31, 2023
multiqc 2
- initial FastQC results for Acer CCC samples (untrimmed) • June 1, 2023
- installing MultiQC on pegasus • June 1, 2023
parallel 1
stats 1
- Notes on GLMs • August 20, 2024
stress hardening 2
- notes on alignment tools • June 14, 2023
- some wins against Pegasus • June 7, 2023
temperaturevariability2023 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
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
venn diagrams 1
- Venn Diagrams • November 22, 2022
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