Files in bioinfonerd/TFenricher
Gene Set Enrichment Analysis for Transcription Factors from NGS Expression Data
DESCRIPTION
DESeq2_all.R
NAMESPACE
O2_script.R
R/DGE_functions.R
R/GSEA_functions.R
R/analysis_functions.R
R/tf-gsea.R
R/txt_to_gmt.R
R/visualizations.R
R/workflow_functions.R
README.md
Results/Differential_Gene_Analysis/DESeq2/DGE1_DGE2_JAK2_ALL_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/DGE1_DGE2_JAK2_ALL_DGEcond_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/DGE1_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/DGE1_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/DGE2_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/DGE2_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsv
Results/Differential_Gene_Analysis/DESeq2/JAK2_DGE1_DGE2_meta_DESeq2.tsv
Results/Differential_Gene_Analysis/DESeq2/PRKCE_DGE1_DGE2_meta_DESeq2.tsv
Results/Differential_Gene_Analysis/DESeq2/SIK3_DGE1_DGE2_meta_DESeq2.tsv
Results/Differential_Gene_Analysis/EdgeR/JAK2_DGE1_DGE2_meta_glmFit_EdgeR.tsv
Results/Differential_Gene_Analysis/EdgeR/JAK2_DGE1_DGE2_meta_qlmFit_EdgeR.tsv
Results/Differential_Gene_Analysis/EdgeR/PRKCE_DGE1_DGE2_meta_EdgeR.tsv
Results/Differential_Gene_Analysis/EdgeR/SIK3_DGE1_DGE2_meta_EdgeR.tsv
Results/Gene_Set_Enrichment_Analysis/DESeq2/JAK2_DGE1_DGE2_meta_DESeq2all_plusISG.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DGEcond_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DGEcond_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DGEcond_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_DGE2_JAK2_ALL_DGEcond_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE1_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_JAK2_JAK2_Target_JAK2_NOT_JAK2_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvactivation.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvactivation_&_repression.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvall.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/DGE2_Target_SIK3_SIK3_Target_SIK3_NOT_SIK3_DESeq2results.tsvrepressive.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/EdgeR/JAK2_DGE1_DGE2_meta_DESeq2all_plusISG.gmtDESeq2.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/EdgeR/JAK2_DGE1_DGE2_meta_glmFit_EdgeRall_plusISG.gmtEdgeR.p_adjusted.tsv
Results/Gene_Set_Enrichment_Analysis/EdgeR/JAK2_DGE1_DGE2_meta_qlmFit_EdgeRall_plusISG.gmtEdgeR.p_adjusted.tsv
TFenricher.Rproj
data/DGE1_DGE2_counts.csv
data/DGE_data/DGE1_DGE2_counts.csv
data/DGE_data/DGE1_DGE2_meta.csv
data/DGE_data/DGE1_postqc-counts.csv
data/DGE_data/DGE1_postqc-meta.csv
data/DGE_data/DGE2_postqc-counts.csv
data/DGE_data/DGE2_postqc-meta.csv
data/DGE_data/data/dge1_dge2_counts.csv
data/DGE_data/data/dge1_dge2_meta.csv
data/DGE_data/data/drug_tas.csv.gz
data/IndraBot_SIK3_Results.tsv
data/TAS_Profile/drug_similarity_filtered.csv
data/TAS_Profile/drug_similarity_raw.csv
data/TAS_Profile/drug_tas.csv
data/TAS_Profile/liganded_genes.csv
data/TF_GSEA_GMT_FILES/activation.gmt
data/TF_GSEA_GMT_FILES/activation_and_repression.gmt
data/TF_GSEA_GMT_FILES/all.gmt
data/TF_GSEA_GMT_FILES/all_plusISG.gmt
data/TF_GSEA_GMT_FILES/repressive.gmt
data/dge1_dge2_meta.csv
data/drug_tas.csv.gz
data/isg.gmt
data/isg.gmx
data/isg.txt
data/postqc-counts.csv
data/postqc-meta.csv
data/target_comb_deseq_results_binary_design.csv
edgeR-analysis.R
example.R
man/hello.Rd
vignettes/ArtemvsNathan-v1_code.Rmd
vignettes/TFEnricher-Analysis-Example.Rmd
vignettes/TFEnricher-Example.Rmd
vignettes/data/dge1_dge2_counts.csv
vignettes/data/dge1_dge2_meta.csv
vignettes/data/drug_tas.csv.gz
