()  () Cgigas (1) Dermo (1) FetchNGS (1) GSEA (1) HPC-server (1) Klone (10) NextFlow (1) NextFlow (1) Perkinsus (1) RNA-seq (2) RNAseq (4) TAG-seq (2) UW-resources (1) WGBS (2) abundance () adapter (2) aws (3) ceasmallr (1) denovotranscript (4) differential (1) differential-abundance (1) differentialabundance (1) fastp (2) fetchngs (2) genome-versions (1) identifiers (1) klone (3) meetings (1) methylseq (3) name-conversion (1) nextflow (14) nf-core (4) params (1) pca (2) perkinsus (1) project-setup (1) referencetranscript (1) rnaseq (4) seqera (3) test (1) virginica (2)

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 Cgigas (1)

Running RNAseq pipeline with reference transcript for C.Gigas Dataset

 Dermo (1)

Re-run FetchNGS for Cvirg_Perkinsus_RNAseq

 FetchNGS (1)

Re-run FetchNGS for Cvirg_Perkinsus_RNAseq

 GSEA (1)

Creating a GMT file to use with GSEA

 HPC-server (1)

UW bioinformatic resources and project set-up

 Klone (10)

Exploring nf-core differential abundance workflow
Re-run FetchNGS for Cvirg_Perkinsus_RNAseq
Run methylseq on Klone
Run RNAseq on perkinsus datasets
Run RNAseq on perkinsus datasets
Run denovotranscript on Klone attempt 3
Run denovotranscript on Klone attempt 2
Running RNAseq pipeline with reference transcript for C.Gigas Dataset
Run denovotranscript on Klone
Sept. 25, 2024 Set up nextflow on UW Klone and run fetchngs

 NextFlow (1)

Creating a Nextflow pipeline for gene count analysis

 NextFlow (1)

Creating a Nextflow pipeline for gene count analysis

 Perkinsus (1)

Re-run FetchNGS for Cvirg_Perkinsus_RNAseq

 RNA-seq (2)

Reprocess TAG-seq data with different FastP parameters
Generic run with nf-core FetchNGS

 RNAseq (4)

Run nf-core differentialabundance pipeline on _C.virg_ data
Run RNAseq on perkinsus datasets
Run RNAseq on perkinsus datasets
Running RNAseq pipeline with reference transcript for C.Gigas Dataset

 TAG-seq (2)

Reprocess TAG-seq data with different FastP parameters
Generic run with nf-core FetchNGS

 UW-resources (1)

UW bioinformatic resources and project set-up

 WGBS (2)

Run ceasmallr (C. virginica) WGBS data through nf-core methylseq pipeline
Reproduce Oyster WGBS analysis with nf-core methylseq

 abundance ()

 adapter (2)

Reprocess TAG-seq data with different FastP parameters
Generic run with nf-core FetchNGS

 aws (3)

Run Seqera rnaseq pipeline for C. gigas study
Run Seqera fetchngs pipeline for C. gigas study
AWS Batch compute environment on Seqera

 ceasmallr (1)

Run ceasmallr (C. virginica) WGBS data through nf-core methylseq pipeline

 denovotranscript (4)

Run methylseq on Klone
Run denovotranscript on Klone attempt 3
Run denovotranscript on Klone attempt 2
Run denovotranscript on Klone

 differential (1)

Creating a GMT file to use with GSEA

 differential-abundance (1)

Exploring nf-core differential abundance workflow

 differentialabundance (1)

Run nf-core differentialabundance pipeline on _C.virg_ data

 fastp (2)

Reprocess TAG-seq data with different FastP parameters
Generic run with nf-core FetchNGS

 fetchngs (2)

Run Seqera fetchngs pipeline for C. gigas study
Sept. 25, 2024 Set up nextflow on UW Klone and run fetchngs

 genome-versions (1)

Compare genes after CGI id conversion attempt 1

 identifiers (1)

Compare genes after CGI id conversion attempt 1

 klone (3)

Run methylseq on Mchilensis WGBS data
Reproduce Oyster WGBS analysis with nf-core methylseq
Repoint nf-core projectDir to srlab directory

 meetings (1)

SW-ES Meeting Summaries

 methylseq (3)

Run methylseq on Mchilensis WGBS data
Run ceasmallr (C. virginica) WGBS data through nf-core methylseq pipeline
Reproduce Oyster WGBS analysis with nf-core methylseq

 name-conversion (1)

Compare genes after CGI id conversion attempt 1

 nextflow (14)

Exploring nf-core differential abundance workflow
Re-run FetchNGS for Cvirg_Perkinsus_RNAseq
Repoint nf-core projectDir to srlab directory
Run methylseq on Klone
Run Seqera rnaseq pipeline for C. gigas study
Run Seqera fetchngs pipeline for C. gigas study
AWS Batch compute environment on Seqera
Run RNAseq on perkinsus datasets
Run RNAseq on perkinsus datasets
Run denovotranscript on Klone attempt 3
Run denovotranscript on Klone attempt 2
Running RNAseq pipeline with reference transcript for C.Gigas Dataset
Run denovotranscript on Klone
Sept. 25, 2024 Set up nextflow on UW Klone and run fetchngs

 nf-core (4)

Run methylseq on Mchilensis WGBS data
Run nf-core differentialabundance pipeline on _C.virg_ data
Run ceasmallr (C. virginica) WGBS data through nf-core methylseq pipeline
Repoint nf-core projectDir to srlab directory

 params (1)

Reproduce Oyster WGBS analysis with nf-core methylseq

 pca (2)

Using ChatGPT to explore thermal resilience based on gene counts
PCA for gene count comparison between NCBI Crassostrea gigas Annotation Release 101 and GCF_963853765.1-RS_2024_06 reference genomes

 perkinsus (1)

Run nf-core differentialabundance pipeline on _C.virg_ data

 project-setup (1)

UW bioinformatic resources and project set-up

 referencetranscript (1)

Running RNAseq pipeline with reference transcript for C.Gigas Dataset

 rnaseq (4)

Using ChatGPT to explore thermal resilience based on gene counts
PCA for gene count comparison between NCBI Crassostrea gigas Annotation Release 101 and GCF_963853765.1-RS_2024_06 reference genomes
Run Seqera rnaseq pipeline for C. gigas study
AWS Batch compute environment on Seqera

 seqera (3)

Run Seqera rnaseq pipeline for C. gigas study
Run Seqera fetchngs pipeline for C. gigas study
AWS Batch compute environment on Seqera

 test (1)

AWS Batch compute environment on Seqera

 virginica (2)

Run nf-core differentialabundance pipeline on _C.virg_ data
Run ceasmallr (C. virginica) WGBS data through nf-core methylseq pipeline