first draft finished

halexand · Nov 21, 2015 · 42f0c82 · 42f0c82
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diff --git a/Figures/v1/Figure1.pdf → Figures/Diatom_Spearman.pdf b/Figures/v1/Figure1.pdf → Figures/Diatom_Spearman.pdf
diff --git a/Figures/Haptophyte_Spearman.pdf b/Figures/Haptophyte_Spearman.pdf
diff --git a/Figures/v1.zip b/Figures/v1.zip
diff --git a/Figures/v1/Comparison_McKewGenes_labeled.pdf b/Figures/v1/Comparison_McKewGenes_labeled.pdf
diff --git a/Figures/v1/Figure1_nutrients.pdf b/Figures/v1/Figure1_nutrients.pdf
diff --git a/Figures/v1/Figure1_v1.pdf b/Figures/v1/Figure1_v1.pdf
diff --git a/Figures/v1/Figure2_v1.pdf b/Figures/v1/Figure2_v1.pdf
diff --git a/Figures/v1/Figure3_PCA.pdf b/Figures/v1/Figure3_PCA.pdf
diff --git a/Figures/v1/Figure3_example.pdf b/Figures/v1/Figure3_example.pdf
diff --git a/Figures/v1/Figure4_v1_Comparison_McKewGenes_labeled.pdf b/Figures/v1/Figure4_v1_Comparison_McKewGenes_labeled.pdf
diff --git a/Figures/v1/SupplementalFigure_APAperChlorophyll.pdf b/Figures/v1/SupplementalFigure_APAperChlorophyll.pdf
diff --git a/Figures/v1/SupplementalFigure_AnnotationOfCommonGenes_v1.pdf b/Figures/v1/SupplementalFigure_AnnotationOfCommonGenes_v1.pdf
diff --git a/Figures/v1/SupplementalFigure_GeneDistrubtion.pdf b/Figures/v1/SupplementalFigure_GeneDistrubtion.pdf
diff --git a/Figures/v1/SupplementalFigure_KOG_Distribution_AcrossTranscriptomes.pdf b/Figures/v1/SupplementalFigure_KOG_Distribution_AcrossTranscriptomes.pdf
diff --git a/Figures/v1/SupplementalFigure_MANTA_Gene_Isoform.pdf b/Figures/v1/SupplementalFigure_MANTA_Gene_Isoform.pdf
diff --git a/Figures/v1/SupplementalFigure_MANTA_Gene_Isoform.png b/Figures/v1/SupplementalFigure_MANTA_Gene_Isoform.png
diff --git a/Figures/v1/SupplementalFigure_MckewATP_Carbon.pdf b/Figures/v1/SupplementalFigure_MckewATP_Carbon.pdf
diff --git a/Figures/v1/SupplementalFigure_MckewCarbonNucleotideAminoAcid_annotated.pdf b/Figures/v1/SupplementalFigure_MckewCarbonNucleotideAminoAcid_annotated.pdf
diff --git a/Figures/v1/SupplementalFigure_SharedGeneComp.pdf b/Figures/v1/SupplementalFigure_SharedGeneComp.pdf
diff --git a/Figures/v1/SupplementalFigure_SpearmanRank_v1.pdf b/Figures/v1/SupplementalFigure_SpearmanRank_v1.pdf
diff --git a/Figures/v1/SupplementalFigure_VennExplanation.jpg b/Figures/v1/SupplementalFigure_VennExplanation.jpg
diff --git a/Figures/v1/SupplementalFigure_Venn_DEGenes.pdf b/Figures/v1/SupplementalFigure_Venn_DEGenes.pdf
diff --git a/Figures/v1/SupplementalFigure_core_changes_v1.pdf b/Figures/v1/SupplementalFigure_core_changes_v1.pdf
diff --git a/Figures/v1/SupplementalFigure_nutrients_v1.pdf b/Figures/v1/SupplementalFigure_nutrients_v1.pdf
diff --git a/TranscriptomeAnnotation/Ehux_CompositePie.pdf b/TranscriptomeAnnotation/Ehux_CompositePie.pdf
diff --git a/TranscriptomeAnnotation/Functional Annotation of Ehux based on KEGG-NewCore.ipynb b/TranscriptomeAnnotation/Functional Annotation of Ehux based on KEGG-NewCore.ipynb
diff --git a/TranscriptomeAnnotation/Functional Annotation of Ehux based on KEGG.ipynb b/TranscriptomeAnnotation/Functional Annotation of Ehux based on KEGG.ipynb
diff --git a/TranscriptomeAnnotation/PercentNumber_BarPlot.pdf b/TranscriptomeAnnotation/PercentNumber_BarPlot.pdf
diff --git a/TranscriptomeAnnotation/Total_BarPlot.pdf b/TranscriptomeAnnotation/Total_BarPlot.pdf
diff --git a/output_RSEM_Bowtie2/APA.xlsx b/output_RSEM_Bowtie2/APA.xlsx
diff --git a/output_RSEM_Bowtie2/Ehux_SigGenes-isoformOrhtologusGroupComparison.ipynb b/output_RSEM_Bowtie2/Ehux_SigGenes-isoformOrhtologusGroupComparison.ipynb
diff --git a/output_RSEM_Bowtie2/MANTA.ipynb b/output_RSEM_Bowtie2/MANTA.ipynb
diff --git a/output_RSEM_Bowtie2/MANTA_Gene_Isoform.pdf b/output_RSEM_Bowtie2/MANTA_Gene_Isoform.pdf
diff --git a/output_RSEM_Bowtie2/MANTA_Gene_Isoform.png b/output_RSEM_Bowtie2/MANTA_Gene_Isoform.png
diff --git a/output_RSEM_Bowtie2/McKewGenesTargets/ATP_synth.tab b/output_RSEM_Bowtie2/McKewGenesTargets/ATP_synth.tab
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