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WA genotyping + some MA troubleshooting (because of course)
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Finishing MA genotyping
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Returning to ACTUAL genotyping
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Supplementing the lipidomics analysis
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Returning to genotyping troubleshooting (Part 2)
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Returning to genotyping troubleshooting
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Correlating WCNA modules
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Integrating all analyses
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Digging into enrichment data
Read More
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Linear mixed effects models for TTR
Read More
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Pairwise lipidomics enrichment
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Lipidomics enrichment
Read More
Lipidomics WCNA
Read More
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Reworking lipidomics analysis
Read More
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(Somewhat) finalized pathway analysis methods
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Analyzing WA crab TTR data
Read More
BAT_correlating
Read More
DMR-DEG overlaps
Read More
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Trying some lipid blanks standards
Read More
Experiment log: WA experiment
Read More
Developing a lipid assay
Read More
Experiment log: WA acclimation
Read More
Analyzing TTR data for MA crabs
Read More
Genotyping MA crabs (back in troubleshooting land)
Read More
Genotyping MA crabs (but now it’s hell)
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Experiment log: WA crabs!
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Experiment log: experiment week!
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Genotyping MA crabs
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Experiment log: Acclimation week
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Characterizing DMR locations
Read More
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We have experimental animals!
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Testing the restriction digest
Read More
Temperature tweaks and setting up the cold room
Read More
PCR optimization
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Picking a restriction enzyme
Read More
Making it even colder
Read More
Testing new primers
Read More
Finishing genotyping
Read More
Checking on temperatures
Read More
Designing a restriction digest
Read More
Characterizing the general methylation landscape with the new genome
Read More
Returning to the killifish project (again)
Read More
Starting the 2024 experiments
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Troubleshooting sample 72
Read More
Rerunning samples on a gel
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Extraction, PCR, and gel for remaining crabs
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Extraction, PCR, and gel for remaining crabs
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Extraction, PCR, and gel for remaining crabs
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Extraction, PCR, and gel to “redo” crabs
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Continued layover in contamination station
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Results from genotyping round 2
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Contamination station round 3
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PCR and gel for TTR crabs
Read More
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Extractions, PCR, and gel for TTR crabs
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Extractions, PCR, and gel for TTR crabs
Read More
Some notes
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Enrichment, enrichment
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Analyzing changes in the maximum number of transcripts expressed
Read More
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Extractions, PCR, and gel for TTR crabs
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Extractions, PCR, and gel for TTR crabs
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Continuing gene activity analyses
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Extractions, PCR, and gel for TTR crabs
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Extractions, PCR, and gel for TTR crabs
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PCR and gel for TTR crabs
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Extractions, PCR, and gel for respirometry + TTR crabs
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Extractions, PCR, and gel for respirometry + TTR crabs
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Testing out new SMC primers
Read More
Testing out new SMC primers
Read More
GLM for respirometry data
Read More
Individual-level analyses
Read More
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Experimental design edits
Read More
A reason for decontamination station
Read More
Simplifying the demographic data analysis
Read More
Still at decontamination station
Read More
Moving past decontamination station (for now)
Read More
Revising analyses
Read More
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Preliminary lipidomics analysis
Read More
Read More
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Revisiting genotypes
Read More
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Extractions, PCR, and gel for respirometry + TTR crabs
Read More
Modifying respirometry analysis
Read More
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Genotyping respirometry crabs
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Preliminary analyses for 2023 experiment
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Re-doing extractions, PCR, and gel for respirometry crabs
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Extractions, PCR, and gel with third set of respirometry crabs
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Extractions, PCR, and gel with second set of respirometry crabs
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Re-trying extractions, PCR, and gel
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Revising respirometry analysis
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Re-trying PCR
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Analyzing respirometry data (finally)
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Treatment Days 33-39
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Treatment Days 27-31
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Treatment Days 23-26
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Treatment Days 21-22
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Treatment Days 16-20
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Treatment Days 14-15
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Treatment Days 10-13
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Treatment Days 7-9
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Treatment Days 1-6
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Acclimation Day 4 and 5
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Experiment is UNDERWAY
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The final countdown (for the Hawaii paper)
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Finalized facility set-up
Read More
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Starting facility set-up
Read More
Finishing the demographic data analysis
Read More
Experiment planning update!
Read More
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Waterproof labelling system (I hope)
Read More
Polynomial terms in transcriptional noise analysis
Read More
Time-to-right analysis
Read More
Survival analysis
Read More
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Transcriptional noise analysis
Read More
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Analyzing demographic data
Read More
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Pathway analysis for RNA-Seq data
Read More
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Global methylation differences by population
Read More
Alternative splicing analyses
Read More
Gene methylation and expression mixOmics
Read More
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Correlating gene methylation and expression
Read More
Continuing with the new genome
Read More
Re-align to the new genome
Read More
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Temperature conditions within tanks
Read More
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Treatment Days 18 through 22
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Treatment Days 15 through 17
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Treatment Days 11 through 14
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Genomic locations of DML
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Treatment Days 8 through 10
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Treatment Days 5 through 7
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Treatment Days 3 and 4
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Treatment Days 1 and 2
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Acclimation Day 5 and 6
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Acclimation Day 3 and 4
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Acclimation Day 2
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Final set up + Day 1!
Read More
Setting up the experimental facility
Read More
Wrapping up the initial methylation analysis
Read More
Digging into DMR
Read More
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Respirometry trial
Read More
Removing L4 samples
Read More
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Revised DMR identification
Read More
Gene expression variability analyses
Read More
Revisiting DMR identification
Read More
Messing around with DMR identification
Read More
Methylation landscape analysis
Read More
Identifying DMR
Read More
Figuring out my BAT_overview
issues
Read More
Moving forward with summarizing methylation
Read More
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General methylation landscape comparisons
Read More
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Trying to tune the sPLS
Read More
Continuing sample alignment
Read More
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Full sample alignment
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Exon methylation and expression
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Continuing mapping tests
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Mapping RRBS data
Read More
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Documenting for posterity (because it’s an annoying process)
Read More
Thinking about SNPs
Read More
Trimming RRBS data
Read More
Starting a new project!
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Miscellaneous enrichment investigations
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Gene librarian for genes with DML associated with enriched GOterms
Read More
Digging into enrichment results
Read More
Protocol for care during non-experimental time
Read More
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Addressing reading committee edits
Read More
Miscellaneous analyses
Read More
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Revising methylKit
parameters
Read More
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Trying topGO
for GOterm enrichment
Read More
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Restarting functional annotation with blastx
Read More
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Functional annotation for new C. gigas genome
Read More
Trying DSS
for DML identification
Read More
Reworking pH-DML
Read More
Running randomization tests on mox
Read More
Investigating methylation data
Read More
Messing around with methylKit
DML settings
Read More
Working with BS-Snper
SNPs
Read More
Characterizing DML
Read More
Characterizing general methylation landscape
Read More
Comparative analysis with methylKit
Read More
Generating genome feature tracks
Read More
Troubleshooting R Studio server session timeouts
Read More
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methylKit
with R Studio server on mox
Read More
Running R scripts on mox
(for real this time)
Read More
Running R scripts on mox
Read More
Preparing to R scripts on mox
Read More
Separating female and indeterminate samples
Read More
Testing base methylKit
code
Read More
Identifying SNPs with BS-Snper
Read More
Identifying SNPs
Read More
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Merging BAM files
Read More
Reviewing revised alignments
Read More
Processing Roslin alignments
Read More
Testing methylKit
parameters
Read More
Preliminary DML identification
Read More
WGS resequencing quote
Read More
Preliminary methylation investigation
Read More
Reviewing bismark
output
Read More
Aligning to the new C. gigas genome
Read More
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Evaluating bismark
output
Read More
Starting bismark
with Manchester data
Read More
Sending samples for sequencing
Read More
Reviewing trimgalore
output with multiqc
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trimgalore
output and fastqc
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Analyzing the full dataset
Read More
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Reviewing second round of trimming
Read More
Revisiting trimming
Read More
Checking trimmed data and starting bismark
Read More
Trimming Hawaii data
Read More
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Investigating methylation island characteristics
Read More
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Extracting DNA and RNA from sperm samples
Read More
Testing protocol for sperm samples
Read More
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Returning to contingency tests
Read More
Re-extracting female samples 16 and 35
Read More
General methylation calculations
Read More
Checking female DNA quality
Read More
Checking female RNA quality
Read More
Checking female DNA and RNA quality
Read More
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Remaining female DNA and RNA extractions
Read More
Subsampling remaining female tissue
Read More
Tweaking Zymo MicroPrep Kit protocols
Read More
Yields from Zymo MicroPrep Kit test samples
Read More
Testing the Zymo MicroPrep Kit (again)
Read More
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Revisiting the manuscript
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Finishing ethanol precipitations
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DNA elution and ethanol precipitation (again)
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MBD-Biotin wash and binding (again) and ethanol precipitations
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DNA elution and ethanol precipitation
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MBD-Biotin wash and binding
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Final quality check
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Final shearing and quality checks
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Ethanol precipitations
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Checking samples on the BioAnalyzer
Read More
Continuing shearing and quality checks
Read More
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More planning for WGBS
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DMC locations and cleaning up scripts
Read More
Planning for WGBS
Read More
Re-shearing DNA and checking quality
Read More
Small tasks to complete the manuscript
Read More
Another QC check before enrichment
Read More
Additional sample preparation
Read More
Prepping for C. virginica sperm MBD Enrichment
Read More
Plan of attack for the mountain of labwork
Read More
Another (and hopefully final) iteration of union bedgraph analyses
Read More
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Checking stacked barplots and post-hoc tests
Read More
Refining multivariate and modeling approaches
Read More
Preliminary follow-up GLMs
Read More
Multivariate analysis for compositional data
Read More
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Fixing characterization code and remaking barplots
Read More
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Genome features and running the CpG characterization pipeline (again)
Read More
Statistical comparisons for methods
Read More
Reworking flanking and intergenic regions
Read More
Revamping distribution plots and creating genome feature plots
Read More
Characterizing union bedgraphs
Read More
More feature tracks
Read More
Revisiting CpG distributions
Read More
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CpG distributions
Read More
Characterizing CpGs in 5x data
Read More
Small tasks for future analyses
Read More
Retroactively obtaining checksums
Read More
Characterizing full samples
Read More
Modifying the CpG characterization pipeline
Read More
Finalizing genome feature tracks
Read More
More genome feature tracks
Read More
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Comparing methylation analysis methods for two coral species
Read More
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Epigenetics reading group feedback!
Read More
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Reframing my questions and making a poster
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C. gigas vs. C. virginica: DML
Read More
C. gigas vs. C. virginica: general methylation landscapes
Read More
Comparing Crassostrea spp. methylation patterns
Read More
C. gigas RNA and DNA extractions: Day 1
Read More
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Looking at labwork and sequencing options
Read More
Gearing up for C. gigas labwork
Read More
Tying up loose ends for the C. virginica gonad paper
Read More
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My last (I promise) analyses
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Adding GOslim annotations to genes
Read More
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Addressing collaborator feedback
Read More
One last set of analyses before dedicated writing
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Further DML annotations
Read More
Preliminary data for PCSGA
Read More
Finalizing the analysis pipeline
Read More
Looking at preliminary DML
Read More
Rerunning bismark
and starting with methylKit
Read More
Fixing my bismark
script for Mox
Read More
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Testing bismark
parameters for WGBS data
Read More
Characterizing GOslim terms
Read More
Enrichment and description of differentially methylated genes
Read More
Identifying differentially methylated genes
Read More
Starting the differentially methylated gene analysis
Read More
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Gene enrichment with GO-MWU
Read More
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Things I did at FHL that were not my research
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Gene enrichment and description
Read More
Gene annotation tables
Read More
Reworking DMR
Read More
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Finalizing C. virginica tracks and revisiting analyses
Read More
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Even more troubleshooting with IGV
Read More
Continued troubleshooting
Read More
Teaching students about oysters and ocean acidification
Read More
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Revised finalized general methylation trends
Read More
Finalized general methylation trends
Read More
Refining general methylation trends
Read More
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Describing general methylation trends
Read More
Revisiting DML analyses
Read More
Resolving DML and DMR visualization issues
Read More
Visualizing DML and DMR
Read More
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Isolating and quantifying C. virginica sperm DNA
Read More
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Gene enrichment for mRNA overlaps
Read More
Continuing isopropanol precipitations
Read More
Preparing C. gigas DNA for WGBS
Read More
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Examining sample clustering
Read More
Proportion test results
Read More
Overlaps with methylKit
gene background
Read More
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Final unconstrained and constrained ordinations
Read More
Protein abundance and environmental data NMDS
Read More
Flanking analysis for mRNA coding regions
Read More
Revisiting NMDS for protein abundance data
Read More
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Mox update
Read More
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Tiling window analysis in methylKit
Read More
Different mincov
values in methylKit
Read More
Running bismark
on Mox
Read More
Testing methylKit
parameters
Read More
Read More
Testing bismark
parameters
Read More
Read More
Read More
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Gene Enrichment Results from compGO
Read More
DML-mRNA Gene Enrichment Results
Read More
DML-mRNA Gene Enrichment
Read More
Blasting for Uniprot codes (again)
Read More
Protocol test: Round 4
Read More
T-24 days until classes…
Read More
Plan for another protocol test
Read More
Microscopes and the Fish Collection
Read More
Teaching students about cryptobenthic reef fish!
Read More
Protocol test: Round 3
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Protocol test: Round 2
Read More
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Today’s hilarious labwork fail
Read More
The last month of this academic year :0
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Assumptions and p-values
Read More
lmers and glmers
Read More
Blasting for Uniprot codes
Read More
flankBed 101
Read More
Quantifying proportion of overlaps
Read More
Understanding gene enrichment
Read More
Finding overlaps between DMLs and other things
Read More
Another month, another set of dreams
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Revised salinity data!
Read More
Preparing for discoveries
Read More
Note to self: Always double check things
Read More
A new enchilada
Read More
A revised enchilada
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Revising environmental data
Read More
A spoiled enchilada
Read More
The whole enchilada (but better this time)
Read More
Reproducibility rodeo
Read More
I am Jerry Gergich
Read More
Visualizing bismark
outputs
Read More
The whole enchilada
Read More
What are those?!
Read More
The meme has evolved
Read More
CCC: Carbonate Chemistry Calculations
Read More
M&M: methylKit and MACAU
Read More
Having pH in mV makes no sense
Read More
The end of a pipeline test
Read More
When the stars (and sequences) align
Read More
Preparing a genome (and my brain)
Read More
Quality: controlled
Read More
Yaamini vs. Computers
Read More
Time to analyze the C. virginica data
Read More
I have water chemistry data!
Read More
Things to do if I had infinite research money
Read More
April showers = More writing hours
Read More
The curious case of the catalase(s)
Read More
Do I have a story for my larval data?
Read More
Another classification revision
Read More
GLMs are neat
Read More
I think I understand classification better now
Read More
[Insert something witty about March Madness]
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This series has (finally) come to an end
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Digital drawing board: Round 2
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Tying up (more) loose ends
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i.e. My grand return to RStudio
Read More
The many paths to school
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Taught sixth grade science today!
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Tryna make the most out of this short month
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Rinse and repeat
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Dynabeads are dynamite
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A fulfilling day of labwork!
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I pimped out my notebook!
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All systems go on C. Virginica sequencing!
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Histology is not an exact science
Read More
I guess break is over…
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The growth data wasn’t very interesting
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I see the light
Read More
Triple-nested for loops are not fun
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a.k.a. How to take a break from proteomics
Read More
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The last bit of data!
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Yesterday’s meeting notes
Read More
Some more regressions
Read More
Connecting the dots
Read More
Following through on my plan
Read More
Quick journey into Manchester world
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My final NMDS
Read More
Visualizing environmental and biomarker data
Read More
Column comparisons
Read More
More data, more problems…?
Read More
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Looked into ROC curves
Read More
I’ve got the power
Read More
Investigating those bad samples
Read More
All lab notebook links are now fixed
Read More
Science doesn’t take a day off
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I have significant results?!
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Everything at the peptide level
Read More
Read More
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The end of a saga
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a.k.a. An excuse to make mini apple pie cheesecakes
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Better results?
Read More
Maybe I should have called this series “Troubleshooting”…
Read More
I finally have technical replication I kinda trust?!
Read More
Dead ends and new plans
Read More
Things DO get better! (Kind of)
Read More
Continuing the PRTC confusion
Read More
I tried doing something statistically impossible today
Read More
Step 1: R-squared Cutoffs
Read More
Are some transitions worse than others?
Read More
R&R: Review and Reproduce
Read More
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We interrupt your regularly scheduled lab notebook perusing for some maintenance.
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One script, infinite boxplots
Read More
Another Skyline saga
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Retracing my steps
Read More
Everything sucks.
Read More
R Help is Helpful
Read More
All aboard the NMDS Struggle Bus
Read More
…Everybody Everywhere
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Clean up, clean up
Read More
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The end.
Read More
We have a Game Plan
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The Final Countdown
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They’re still not growing!
Read More
Checked the 80 micron screen again
Read More
Totes are pesky
Read More
Immersion heaters are pesky
Read More
Anoxia is no bueno
Read More
Smooth Saturday screening
Read More
Lots of maintenance today
Read More
My larvae are 60 microns now!
Read More
Counting larvae takes a while
Read More
A bit of a rough start today
Read More
I only have five goals
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I’m the Mother of Oysters
Read More
Spoiler: We have baby oysters!
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NO OYSTERS DIED!
Read More
It’s getting ugly
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The mortalities continue
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Revised for the last time
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My prior calculations were incorrect!
Read More
Featuring reduced crosses and pools
Read More
Temperature is at 23 ºC!
Read More
If you don’t have a visualization, did you really analyze data?
Read More
My samples are DONE.
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Last day of my samples!
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Status quo?
Read More
Murphy’s Law is always relevant
Read More
The power is back!
Read More
Still plugging along
Read More
Power outage edition
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More borrowed PRTC = All samples prepared
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Our assay works!
Read More
It’s SRM assay time!
Read More
WE HAVE OUR TARGETS.
Read More
Those peaks are running interference
Read More
And the pH is low (again)
Read More
I have draft transitions!
Read More
Differential Expression + Protein Function = Targets?
Read More
The pH is kind of stable?
Read More
MSstats works!
Read More
June was rather slow
Read More
It’s time to think about crosses!
Read More
Revised (final?) Conditioning Plan
Read More
Sophie’s New Choice: Temperature, Flow or pH?
Read More
It’s been a slow burn
Read More
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This time it only took 4 hours!
Read More
Remember that Skyline fail?
Read More
From Saturday 6/10 to Wednesday 7/5
Read More
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Time to fatten the oysters up!
Read More
It’s getting hot in here
Read More
Yaamini vs. CentriVap: The Sequel
Read More
(Almost) done with Spring Quarter already?!
Read More
I am now a faster pipetter
Read More
All this protein but I’m still not swole.
Read More
Here’s hoping this is the last round of DNR sample preparation!
Read More
I need to become a faster pipetter.
Read More
We have lots of protein!
Read More
How many times can you restart sample preparation?
Read More
Slice and dice
Read More
More cowbell? More samples.
Read More
The DIA pipeline has been quite a #strugglebus
Read More
It’s always good to practice your methods of torture.
Read More
Who wants to manually quality check peptides?!
Read More
Record scratch. Freeze frame.
Read More
Who are the lucky winners?
Read More
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I can now analyze my full .blib!
Read More
It’s already MAY.
Read More
Skyline works with our demultiplexed files!
Read More
Read More
Laura went out to Manchester today and graciously cleaned my oysters
Read More
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I’m going to get stuff done for Pubathon (I promise)!
Read More
My files are done converting!
Read More
Another new MSConvert CLI
Read More
New MSConvert CLI, hot off the presses
Read More
Demultiplexing is perplexing
Read More
OA System Breakdown
Read More
We’re done with our OA experiment!
Read More
I was so busy catching up on classes I forgot it was April!
Read More
What happened when Laura got stranded in the Midwest
Read More
I’m at NSA, to Grace and Olivia went to Manchester.
Read More
Here’s the evolution of my poster for NSA!
Read More
Checking in before we leave for NSA
Read More
On that number-crunching grind
Read More
We have data!!!
Read More
A couple hiccups at Manchester today
Read More
It works!
Read More
Yesterday I set up a system for cataloging our water chemistry data.
Read More
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New day, same errors
Read More
We’re officially halfway through our pH treatment window!
Read More
To reconvert or not reconvert?
Read More
Hit an obstacle with PECAN this weekend.
Read More
Another smooth day at Manchester!
Read More
:cake: It’s not as easy as pie :cake:
Read More
March Maddness is upon us.
Read More
Today, I spent 3 hours cleaning oyster :poop:
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The OA System is up and running!
Read More
February Goals Update
Read More
Conducted my first outreach activity today!
Read More
First Manchester Sampling
Read More
February Goals
Read More
…But now trouble is gone!
Read More
…And trouble stuck around at 3:51 p.m. on January 29.
Read More
Trouble struck at 8:16 p.m. on January 28.
Read More
My samples are on the Mass Spec!
Read More
Mass Spectrometer Set-up
Read More
M/Z ratios: Mass hysteria ensues
Read More
PRTC: We know what those peptides can be
Read More
Not Salty about Desalting
Read More
Speed Vacuum = Slow Process
Read More
Trippin for Trypsin
Read More
If at first you don’t succeed, trial trial again.
Read More
Practice makes perfect?
Read More
Gill Tissue + Sound Waves = Protein Soup
Read More
My first day in lab was a busy one!
Read More
My DNR project is still on the brain!.
Read More
Now that it’s almost November, it’s time to get cracking on the DNR project.
Read More
As promised, here is some background on my current project
Read More
Hello!
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