29_genes.txt
Counts/
Counts/countdata.csv
Counts/Langfelder_wt_q111_countData.txt
Counts/LangfelderStudy.SVAcorrectedcount.txt
Counts/ThisStudy.SVAcorrectedcount.txt
DEG_lists/
DEG_lists/Hdac2KOvsHdac2WT_HttQ111_3vs1_edgeR_quasilikelihoodFtest.SVA.txt
DEG_lists/Hdac2KOvsHdac2WT_HttWT_4vs2_edgeR_quasilikelihoodFtest.SVA.txt
DEG_lists/HttQ111atHdac2KOvsHttWTHdac2WT_edgeR_quasilikelihoodFtest.SVA.txt
DEG_lists/HttQ111vsWT_KOHdac2_3vs4_edgeR_quasilikelihoodFtest.SVA.txt
DEG_lists/HttQ111vsWT_WTHdac2_2vs1_edgeR_quasilikelihoodFtest.SVA.txt
DEG_lists/LangfelderStudy_edgeR_quasilikelihoodFtest.txt
MetaData/
MetaData/Langfelder_wt_q111_metaData.txt
MetaData/metadata.csv
Mus_musculus_.GRCm38.75.genes_to_remove.txt
Pathways/
Pathways/Hdac2KOvsHdac2WT_HttQ111_3vs1_fdr_down_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttQ111_3vs1_fdr_up_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttQ111_3vs1_nominal_down_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttQ111_3vs1_nominal_up_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttWT_4vs2_fdr_down_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttWT_4vs2_fdr_up_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttWT_4vs2_nominal_down_0.05.FuncAnnotChart.tsv
Pathways/Hdac2KOvsHdac2WT_HttWT_4vs2_nominal_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_fdr_all_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_fdr_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_fdr_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_nominal_all_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_nominal_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111atHdac2KOvsHttWTatHdac2WT_nominal_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_KOHdac2_3vs4_fdr_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_KOHdac2_3vs4_fdr_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_KOHdac2_3vs4_nominal_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_KOHdac2_3vs4_nominal_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_WTHdac2_2vs1_fdr_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_WTHdac2_2vs1_fdr_up_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_WTHdac2_2vs1_nominal_down_0.05.FuncAnnotChart.tsv
Pathways/HttQ111vsWT_WTHdac2_2vs1_nominal_up_0.05.FuncAnnotChart.tsv
assessingDEGoverlapsignificance.R
cleaningP.R
compareThisStudyLangfelderStudy.R
pathwayComparison.R
plot_and_significance_29genes_relativeEffect.R
rescue_effect_analysis.R
runDAVID.R
runEdgeR.Langfelder.R
runEdgeR.SVA.R
