From 054220feccd536ab489f264a3a7c4ba1bf3a0e7e Mon Sep 17 00:00:00 2001
From: aakan96 <aakan96@mi.fu-berlin.de>
Date: Thu, 20 Jul 2023 18:16:35 +0000
Subject: [PATCH] Update 66 files
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- /Differential Expression Analysis/Deseq2/mRNA/GSE20347 mRNA.R
- /Differential Expression Analysis/Deseq2/mRNA/GSE29001 mRNA.R
- /Differential Expression Analysis/Deseq2/mRNA/GSE70409 mRNA.R
- /Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R
- /Differential Expression Analysis/Limma/mRNA/GSE20347.R
- /Differential Expression Analysis/Limma/mRNA/GSE29001.R
- /Differential Expression Analysis/Limma/mRNA/GSE70409.R
- /Differential Expression Analysis/Limma/miRNA/GSE43732.R
- /Differential Expression Analysis/Limma/miRNA/GSE55857.R
- /Differential Expression Analysis/Limma/miRNA/GSE6188.R
- /Differential Expression Analysis/merging/.gitkeep
- /MultiMIR/multimir_results_final.xlsx
- /Data Annotation/GO biological function.png
- /Data Annotation/GO cellular component.png
- /Data Annotation/GO molecular function.png
- /Data Annotation/GO_enrichment.R
- /Data Annotation/biomart_for_annotation.R
- /Data Annotation/go.csv
- /Data Annotation/mrna.csv
- /Machine Learning/.gitkeep
- /Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb
- /Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb
- /Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb
- /Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb
- /Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb
- /Machine Learning/mRNA_DS_preprocessed_training_data.csv
- /Cytoscape/cytoscape.xlsx
- /Cytoscape/extract_mrna_names_from_mirna.R
- /Cytoscape/miRNAmRNA.xlsx
- /Cytoscape/multimir_results.xlsx
- /Cytoscape/new.png
- /Survival Analysis/.gitkeep
- /Survival Analysis/document.pdf
- /01_Differential Expression Analysis/Deseq2/mRNA/GSE70409 mRNA.R
- /01_Differential Expression Analysis/Deseq2/mRNA/GSE29001 mRNA.R
- /01_Differential Expression Analysis/Deseq2/mRNA/GSE20347 mRNA.R
- /01_Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R
- /01_Differential Expression Analysis/Limma/mRNA/GSE29001.R
- /01_Differential Expression Analysis/Limma/mRNA/GSE70409.R
- /01_Differential Expression Analysis/Limma/mRNA/GSE20347.R
- /01_Differential Expression Analysis/Limma/miRNA/GSE55857.R
- /01_Differential Expression Analysis/Limma/miRNA/GSE6188.R
- /01_Differential Expression Analysis/Limma/miRNA/GSE43732.R
- /01_Differential Expression Analysis/merging/.gitkeep
- /02_MultiMIR/multimir_results_final.xlsx
- /05_Data Annotation/GO biological function.png
- /05_Data Annotation/biomart_for_annotation.R
- /05_Data Annotation/GO cellular component.png
- /05_Data Annotation/go.csv
- /05_Data Annotation/GO molecular function.png
- /05_Data Annotation/GO_enrichment.R
- /05_Data Annotation/mrna.csv
- /03_Machine Learning/.gitkeep
- /03_Machine Learning/mRNA_DS_preprocessed_training_data.csv
- /03_Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb
- /03_Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb
- /03_Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb
- /03_Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb
- /03_Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb
- /04_Cytoscape/extract_mrna_names_from_mirna.R
- /04_Cytoscape/miRNAmRNA.xlsx
- /04_Cytoscape/cytoscape.xlsx
- /04_Cytoscape/new.png
- /04_Cytoscape/multimir_results.xlsx
- /06_Survival Analysis/.gitkeep
- /06_Survival Analysis/document.pdf
---
.../mRNA/GSE20347\342\200\213 mRNA\342\200\213.R" | 0
.../mRNA/GSE29001\342\200\213 mRNA\342\200\213.R" | 0
.../mRNA/GSE70409\342\200\213 mRNA\342\200\213.R" | 0
.../Deseq2/miRNA/GSE43732_miRNA_Multimir.R | 0
.../Limma/mRNA/GSE20347.R | 0
.../Limma/mRNA/GSE29001.R | 0
.../Limma/mRNA/GSE70409.R | 0
.../Limma/miRNA/GSE43732.R | 0
.../Limma/miRNA/GSE55857.R | 0
.../Limma/miRNA/GSE6188.R | 0
.../merging/.gitkeep | 0
.../multimir_results_final.xlsx | Bin
{Machine Learning => 03_Machine Learning}/.gitkeep | 0
.../DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb | 0
.../DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb | 0
.../DS_mRNA_limma_dataset_svm_F.ipynb | 0
.../DS_mRNA_limma_dataset_xgb_final-F.ipynb | 0
.../DS_miRNA_limma_dataset_xgb_final-F.ipynb | 0
.../mRNA_DS_preprocessed_training_data.csv | 0
{Cytoscape => 04_Cytoscape}/cytoscape.xlsx | Bin
.../extract_mrna_names_from_mirna.R | 0
{Cytoscape => 04_Cytoscape}/miRNAmRNA.xlsx | Bin
{Cytoscape => 04_Cytoscape}/multimir_results.xlsx | Bin
{Cytoscape => 04_Cytoscape}/new.png | Bin
.../GO biological function.png | Bin
.../GO cellular component.png | Bin
.../GO molecular function.png | Bin
.../GO_enrichment.R | 0
.../biomart_for_annotation.R | 0
{Data Annotation => 05_Data Annotation}/go.csv | 0
{Data Annotation => 05_Data Annotation}/mrna.csv | 0
.../.gitkeep | 0
.../document.pdf | Bin
33 files changed, 0 insertions(+), 0 deletions(-)
rename "Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R" => "01_Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R" (100%)
rename "Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R" => "01_Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R" (100%)
rename "Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R" => "01_Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R" (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Deseq2/miRNA/GSE43732_miRNA_Multimir.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/mRNA/GSE20347.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/mRNA/GSE29001.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/mRNA/GSE70409.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/miRNA/GSE43732.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/miRNA/GSE55857.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/Limma/miRNA/GSE6188.R (100%)
rename {Differential Expression Analysis => 01_Differential Expression Analysis}/merging/.gitkeep (100%)
rename {MultiMIR => 02_MultiMIR}/multimir_results_final.xlsx (100%)
rename {Machine Learning => 03_Machine Learning}/.gitkeep (100%)
rename {Machine Learning => 03_Machine Learning}/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb (100%)
rename {Machine Learning => 03_Machine Learning}/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb (100%)
rename {Machine Learning => 03_Machine Learning}/DS_mRNA_limma_dataset_svm_F.ipynb (100%)
rename {Machine Learning => 03_Machine Learning}/DS_mRNA_limma_dataset_xgb_final-F.ipynb (100%)
rename {Machine Learning => 03_Machine Learning}/DS_miRNA_limma_dataset_xgb_final-F.ipynb (100%)
rename {Machine Learning => 03_Machine Learning}/mRNA_DS_preprocessed_training_data.csv (100%)
rename {Cytoscape => 04_Cytoscape}/cytoscape.xlsx (100%)
rename {Cytoscape => 04_Cytoscape}/extract_mrna_names_from_mirna.R (100%)
rename {Cytoscape => 04_Cytoscape}/miRNAmRNA.xlsx (100%)
rename {Cytoscape => 04_Cytoscape}/multimir_results.xlsx (100%)
rename {Cytoscape => 04_Cytoscape}/new.png (100%)
rename {Data Annotation => 05_Data Annotation}/GO biological function.png (100%)
rename {Data Annotation => 05_Data Annotation}/GO cellular component.png (100%)
rename {Data Annotation => 05_Data Annotation}/GO molecular function.png (100%)
rename {Data Annotation => 05_Data Annotation}/GO_enrichment.R (100%)
rename {Data Annotation => 05_Data Annotation}/biomart_for_annotation.R (100%)
rename {Data Annotation => 05_Data Annotation}/go.csv (100%)
rename {Data Annotation => 05_Data Annotation}/mrna.csv (100%)
rename {Survival Analysis => 06_Survival Analysis}/.gitkeep (100%)
rename {Survival Analysis => 06_Survival Analysis}/document.pdf (100%)
diff --git "a/Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R" "b/01_Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R"
similarity index 100%
rename from "Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R"
rename to "01_Differential Expression Analysis/Deseq2/mRNA/GSE20347\342\200\213 mRNA\342\200\213.R"
diff --git "a/Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R" "b/01_Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R"
similarity index 100%
rename from "Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R"
rename to "01_Differential Expression Analysis/Deseq2/mRNA/GSE29001\342\200\213 mRNA\342\200\213.R"
diff --git "a/Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R" "b/01_Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R"
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rename from "Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R"
rename to "01_Differential Expression Analysis/Deseq2/mRNA/GSE70409\342\200\213 mRNA\342\200\213.R"
diff --git a/Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R b/01_Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R
similarity index 100%
rename from Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R
rename to 01_Differential Expression Analysis/Deseq2/miRNA/GSE43732_miRNA_Multimir.R
diff --git a/Differential Expression Analysis/Limma/mRNA/GSE20347.R b/01_Differential Expression Analysis/Limma/mRNA/GSE20347.R
similarity index 100%
rename from Differential Expression Analysis/Limma/mRNA/GSE20347.R
rename to 01_Differential Expression Analysis/Limma/mRNA/GSE20347.R
diff --git a/Differential Expression Analysis/Limma/mRNA/GSE29001.R b/01_Differential Expression Analysis/Limma/mRNA/GSE29001.R
similarity index 100%
rename from Differential Expression Analysis/Limma/mRNA/GSE29001.R
rename to 01_Differential Expression Analysis/Limma/mRNA/GSE29001.R
diff --git a/Differential Expression Analysis/Limma/mRNA/GSE70409.R b/01_Differential Expression Analysis/Limma/mRNA/GSE70409.R
similarity index 100%
rename from Differential Expression Analysis/Limma/mRNA/GSE70409.R
rename to 01_Differential Expression Analysis/Limma/mRNA/GSE70409.R
diff --git a/Differential Expression Analysis/Limma/miRNA/GSE43732.R b/01_Differential Expression Analysis/Limma/miRNA/GSE43732.R
similarity index 100%
rename from Differential Expression Analysis/Limma/miRNA/GSE43732.R
rename to 01_Differential Expression Analysis/Limma/miRNA/GSE43732.R
diff --git a/Differential Expression Analysis/Limma/miRNA/GSE55857.R b/01_Differential Expression Analysis/Limma/miRNA/GSE55857.R
similarity index 100%
rename from Differential Expression Analysis/Limma/miRNA/GSE55857.R
rename to 01_Differential Expression Analysis/Limma/miRNA/GSE55857.R
diff --git a/Differential Expression Analysis/Limma/miRNA/GSE6188.R b/01_Differential Expression Analysis/Limma/miRNA/GSE6188.R
similarity index 100%
rename from Differential Expression Analysis/Limma/miRNA/GSE6188.R
rename to 01_Differential Expression Analysis/Limma/miRNA/GSE6188.R
diff --git a/Differential Expression Analysis/merging/.gitkeep b/01_Differential Expression Analysis/merging/.gitkeep
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rename from Differential Expression Analysis/merging/.gitkeep
rename to 01_Differential Expression Analysis/merging/.gitkeep
diff --git a/MultiMIR/multimir_results_final.xlsx b/02_MultiMIR/multimir_results_final.xlsx
similarity index 100%
rename from MultiMIR/multimir_results_final.xlsx
rename to 02_MultiMIR/multimir_results_final.xlsx
diff --git a/Machine Learning/.gitkeep b/03_Machine Learning/.gitkeep
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rename from Machine Learning/.gitkeep
rename to 03_Machine Learning/.gitkeep
diff --git a/Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb b/03_Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb
similarity index 100%
rename from Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb
rename to 03_Machine Learning/DS_mRNA_TCGA_limma_dataset_svm_final-F.ipynb
diff --git a/Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb b/03_Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb
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rename from Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb
rename to 03_Machine Learning/DS_mRNA_TCGA_limma_dataset_xgb_final-F.ipynb
diff --git a/Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb b/03_Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb
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rename from Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb
rename to 03_Machine Learning/DS_mRNA_limma_dataset_svm_F.ipynb
diff --git a/Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb b/03_Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb
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rename from Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb
rename to 03_Machine Learning/DS_mRNA_limma_dataset_xgb_final-F.ipynb
diff --git a/Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb b/03_Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb
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rename from Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb
rename to 03_Machine Learning/DS_miRNA_limma_dataset_xgb_final-F.ipynb
diff --git a/Machine Learning/mRNA_DS_preprocessed_training_data.csv b/03_Machine Learning/mRNA_DS_preprocessed_training_data.csv
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rename from Machine Learning/mRNA_DS_preprocessed_training_data.csv
rename to 03_Machine Learning/mRNA_DS_preprocessed_training_data.csv
diff --git a/Cytoscape/cytoscape.xlsx b/04_Cytoscape/cytoscape.xlsx
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rename from Cytoscape/cytoscape.xlsx
rename to 04_Cytoscape/cytoscape.xlsx
diff --git a/Cytoscape/extract_mrna_names_from_mirna.R b/04_Cytoscape/extract_mrna_names_from_mirna.R
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rename from Cytoscape/extract_mrna_names_from_mirna.R
rename to 04_Cytoscape/extract_mrna_names_from_mirna.R
diff --git a/Cytoscape/miRNAmRNA.xlsx b/04_Cytoscape/miRNAmRNA.xlsx
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rename from Cytoscape/miRNAmRNA.xlsx
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diff --git a/Cytoscape/multimir_results.xlsx b/04_Cytoscape/multimir_results.xlsx
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diff --git a/Cytoscape/new.png b/04_Cytoscape/new.png
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diff --git a/Data Annotation/GO biological function.png b/05_Data Annotation/GO biological function.png
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diff --git a/Data Annotation/GO cellular component.png b/05_Data Annotation/GO cellular component.png
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diff --git a/Data Annotation/GO molecular function.png b/05_Data Annotation/GO molecular function.png
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diff --git a/Data Annotation/GO_enrichment.R b/05_Data Annotation/GO_enrichment.R
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diff --git a/Data Annotation/biomart_for_annotation.R b/05_Data Annotation/biomart_for_annotation.R
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rename from Data Annotation/biomart_for_annotation.R
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diff --git a/Data Annotation/go.csv b/05_Data Annotation/go.csv
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diff --git a/Data Annotation/mrna.csv b/05_Data Annotation/mrna.csv
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diff --git a/Survival Analysis/.gitkeep b/06_Survival Analysis/.gitkeep
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rename from Survival Analysis/.gitkeep
rename to 06_Survival Analysis/.gitkeep
diff --git a/Survival Analysis/document.pdf b/06_Survival Analysis/document.pdf
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rename from Survival Analysis/document.pdf
rename to 06_Survival Analysis/document.pdf
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