differential expression analysis with RNAseq data from 15 species of Fundulus killifish following a salinity exposure experiment (FW, BW, transfer)
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DEgenes_multifactor.png
DEgenes_multifactor_whitebg.png
DEgenes_multifactor_whitebg_5genes.png
PCA.png
PCA_clade_nativephysiology_Oct2018.png
PCA_clade_treatment_Oct2018.png
PCA_killifish_clade_species.png
README.md
aqp3_clade1.png
aqp3_clade2.png
aqp_clade3.png
aqu3.png
cftr_clade1.png
cftr_clade2.png
cftr_clade3.png
clock_clade1.png
clock_clade2.png
clock_clade3.png
dispersion_group_condition.png
dispersion_interactionterm.png
killifish_reads_contigs_stats.xlsx
multi-ggplot2-catalog.pdf
multi-ggplot2-catalog_salinity.pdf
multi-ggplot2-catalog_salinity_31Oct2018.pdf
septin2B_clade1.png
septin2b_clade2.png
septin2b_clade3.png
tSNE_names_clade.png
tsne_killifish_clade.png
tsne_killifish_genes.png
tsne_killifish_genes_perp50.png

README.md

RNAseq_15killifish

This repository is a WORK IN PROGRESS

Differential expression analysis with RNAseq data from 16 species of Fundulus killifish following a salinity exposure experiment (FW, BW, transfer).

De novo transcriptome assemblies and annotations for each species are located here:

Johnson, L., & Whitehead, A. (2018, July 16). Fundulus Multispecies Osmotic Transcriptome Sequencing Project (FMOTSP). https://doi.org/10.17605/OSF.IO/M4XEG

Raw data: https://www.ncbi.nlm.nih.gov/bioproject/473009

Analysis scripts: https://github.com/ljcohen/RNAseq_15killifish

See this repository for assembly/evaluation scripts and data.