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test:
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --heatmap --heatmap_colorscheme 'black,yellow'
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --sample_cor_matrix
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --prin_comp 3 --add_prin_comp_heatmaps 5 --Zscale
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --compare_replicates
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --imgfmt svg --boxplot_log2_dist 0.8
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --top_variable_genes 300 --min_across_ANY_samples_gene_expr_val 5 --gene_cor_matrix
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --mean_vs_sd
# head -n11 candidate.Trinity_trans.TMM.EXPR.matrix > test.matrix && ${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m test.matrix -s candidate.samples.txt --per_gene_plots --per_gene_plots_incl_vioplot
${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --heatmap --heatmap_colorscheme 'black,yellow' --order_columns_by_samples_file
touch ./test
clean:
rm -f ./candidate.Trinity_trans.TMM.EXPR.matrix.*
rm -f ./test
rm -f ./test.matrix ./test.matrix.*
rm -f ./*.pdf
rm -f ./*.svg
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