()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  ()  () 514 () ADF&G (1) Correlation (2) DESeq2 (3) DESeq2 (3) DNA (2) GO (1) GO-MWU (8) GO-MWU (8) IDs (1) Jupyter (4) Kallisto (4) PCA (1) PCAs () QERM (1) Trinity () Ubuntu (5) Variable (2) WGCNA (2) WGCNA (2) WordPress (1) archived (1) cbai_transcriptomev2.0 () cbai_transcriptomev4.0 () clustering (5) deseq2 () design () ecology () extraction (2) genes (1) genes (1) goals () hemat_transcriptomev1.6 () hematodinium (7) hematodinium (7) immune (3) immune (3) in (1) interview (1) interview (1) kallisto () linear (2) literature (1) manual (3) modeling (2) modules (1) notes (2) overview () pathology () planning (1) plasticity (1) project (1) protocol (1) samples () taxa (2) vitro (1) writeup (13)

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 514 ()

 ADF&G (1)

Jensen Samples

 Correlation (2)

Correlating Crab Variables, Fixed
Correlating Crab Variables

 DESeq2 (3)

December Goals
Doing It All
Creating PCAs

 DESeq2 (3)

December Goals
Doing It All
Creating PCAs

 DNA (2)

DNA Extraction Results
Extracting DNA from Archived Samples

 GO (1)

GO terms and Venn Diagrams

 GO-MWU (8)

Fixing GO-MWU
Using C. bairdi transcriptome v4.0
Ditching full genomes, using hematodinium transcriptomev1.6
GO-MWU Wrapup + Future Plans
Completed GO-MWU for new analyses
Back to Square One?
Starting GO-MWU
Workflow Standardization

 GO-MWU (8)

Fixing GO-MWU
Using C. bairdi transcriptome v4.0
Ditching full genomes, using hematodinium transcriptomev1.6
GO-MWU Wrapup + Future Plans
Completed GO-MWU for new analyses
Back to Square One?
Starting GO-MWU
Workflow Standardization

 IDs (1)

GO terms and Venn Diagrams

 Jupyter (4)

Orientation 2, This Time It's CoE-ier
Orientation!
Getting A Grep On Things
Probing Jupyter

 Kallisto (4)

Lists of Differentially-Expressed Genes (plus graphs)
Day 0 Ambient vs. Day 17 Ambient
Adding Individual Libraries
Starting Kallisto

 PCA (1)

Immune Genes

 PCAs ()

 QERM (1)

Using Linear Modeling on Hematodinium

 Trinity ()

 Ubuntu (5)

Orientation 2, This Time It's CoE-ier
Orientation!
Getting A Grep On Things
Probing Jupyter
He-Mat and the Masters of the Database

 Variable (2)

Correlating Crab Variables, Fixed
Correlating Crab Variables

 WGCNA (2)

Figuring Out WGCNA, Part 2
Figuring Out WGCNA, Part 1

 WGCNA (2)

Figuring Out WGCNA, Part 2
Figuring Out WGCNA, Part 1

 WordPress (1)

WordPress Management

 archived (1)

Jensen Samples

 cbai_transcriptomev2.0 ()

 cbai_transcriptomev4.0 ()

 clustering (5)

Manually Clustering Immune Genes
Manual Modules 4
Manual Modules 3
Manual Clustering 2
Manual Clustering

 deseq2 ()

 design ()

 ecology ()

 extraction (2)

DNA Extraction Results
Extracting DNA from Archived Samples

 genes (1)

Adaptive Immune Gene Dive

 genes (1)

Adaptive Immune Gene Dive

 goals ()

 hemat_transcriptomev1.6 ()

 hematodinium (7)

WGCNA 4
Reading Update and Research Plans
Orientation 2, This Time It's CoE-ier
Orientation!
Getting A Grep On Things
Probing Jupyter
He-Mat and the Masters of the Database

 hematodinium (7)

WGCNA 4
Reading Update and Research Plans
Orientation 2, This Time It's CoE-ier
Orientation!
Getting A Grep On Things
Probing Jupyter
He-Mat and the Masters of the Database

 immune (3)

Adaptive Immune Gene Dive
Manually Clustering Immune Genes
Immune Genes

 immune (3)

Adaptive Immune Gene Dive
Manually Clustering Immune Genes
Immune Genes

 in (1)

Project Proposal Idea

 interview (1)

Background Info on Grace's Research

 interview (1)

Background Info on Grace's Research

 kallisto ()

 linear (2)

Linear Modeling, for real
Using Linear Modeling on Hematodinium

 literature (1)

Bairdi Immune Genes Lit Search

 manual (3)

Manual Modules 4
Manual Modules 3
Manual Clustering 2

 modeling (2)

Linear Modeling, for real
Using Linear Modeling on Hematodinium

 modules (1)

WGCNA Part 3

 notes (2)

TRINITY Pipeline Update
Reading Update and Research Plans

 overview ()

 pathology ()

 planning (1)

Reading Update and Research Plans

 plasticity (1)

Crab Plasticity

 project (1)

Project Proposal Idea

 protocol (1)

Chatting with Pam Jensen

 samples ()

 taxa (2)

Using NCBI Genomes
Determining Taxa of DEGs

 vitro (1)

Project Proposal Idea

 writeup (13)

November Summary
October Summary
September Summary
January Summary
October Summary
September Summary
January Summary
December Summary
November Summary
September Summary
August Summary
July Summary
June Summary