EBII2024 initial

2024/evaiin1/SingleCell/DEA_GSEA/DEA.metadata.json

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+{
+    "name": "SingleCell_DEA.Rmd",
+    "abstract": "Learn how to perform DEA (Differential Expression Analysis) based on a scaled, normalized, and filtered Seurat object",
+    "author": [
+        {
+            "@type": "Person",
+            "name": "Thibault Dayris",
+            "email": "thibault.dayris@gustaveroussy.fr"
+        }
+    ],
+    "contributor": [
+        {
+            "@type": "Person",
+            "name": "Emilie Drouineau",
+            "email": "emilie.drouineau@cea.fr"
+        }
+    ],
+    "description": "This tutorial let you see all function IO and contains the full verbatim of the EBAII 2023 session",
+    "audiance": {
+        "@type": "Audiance",
+        "audienceType": "beginner command line biologist"
+    },
+    "educationalLevel": "Beginner",
+    "inLanguage": [
+        "en-GB"
+    ],
+    "teaches": [
+        "The student will be able to load Seurat object",
+        "The student will be able to select a DEA method",
+        "The student will be able to select a Seurat count slot",
+        "The student will be able to compose the command line themselves",
+        "The student will be albe to draw basic graphs",
+        "The student will be able to save results as CSV"
+    ],
+    "keywords": "Seurat, R, Differential Expression Analysis",
+    "learningResourceType": [
+        "handout"
+    ],
+    "license": [
+        "https://mit-license.org/"
+    ],
+    "dateModified": "2023-10-25T13:43:27,142911245+02:00"
+}

2024/evaiin1/SingleCell/DEA_GSEA/GSEA.metadata.json

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+{
+    "name": "SingleCell_GSEA.Rmd",
+    "abstract": "Learn how to perform GSEA (Gene Set Enrichment Analysis) based on a scaled, normalized, and filtered Seurat object",
+    "author": [
+        {
+            "@type": "Person",
+            "name": "Thibault Dayris",
+            "email": "thibault.dayris@gustaveroussy.fr"
+        }
+    ],
+    "contributor": [
+        {
+            "@type": "Person",
+            "name": "Emilie Drouineau",
+            "email": "emilie.drouineau@cea.fr"
+        }
+    ],
+    "description": "This tutorial let you see all function IO and contains the full verbatim of the EBAII 2023 session",
+    "audiance": {
+        "@type": "Audiance",
+        "audienceType": "beginner command line biologist"
+    },
+    "educationalLevel": "Beginner",
+    "inLanguage": [
+        "en-GB"
+    ],
+    "teaches": [
+        "The student will be able to load Seurat object",
+        "The student will be able to select a GSEA method",
+        "The student will be able to select a Seurat count slot",
+        "The student will be able to compose the command line themselves",
+        "The student will be albe to draw basic graphs",
+        "The student will be able to save results as CSV"
+    ],
+    "keywords": "Seurat, R, Gene Set Enrichment Analysis",
+    "learningResourceType": [
+        "handout"
+    ],
+    "license": [
+        "https://mit-license.org/"
+    ],
+    "dateModified": "2023-10-25T13:43:27,142911245+02:00"
+}

2024/evaiin1/SingleCell/DEA_GSEA/Makefile

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+
+SHELL=/usr/bin/bash
+.ONESHELL:
+.SHELLFLAGS := -euic
+.DELETE_ON_ERROR:
+MAKEFLAGS += --warn-undefined-variables
+MAKEFLAGS += --no-builtin-rules
+
+.PHONY:
+all: SingleCell_GSEA.html SingleCell_DEA.html
+
+SingleCell_GSEA.html: ebaii SingleCell_DEA.html
+	mamba activate ./ebaii && \
+	R -e 'rmarkdown::render("SingleCell_GSEA.Rmd")'
+
+
+SingleCell_DEA.html: ebaii Scaled_Normalized_Seurat_Object.RDS
+	mamba activate ./ebaii && \
+	R -e 'rmarkdown::render("SingleCell_DEA.Rmd")'
+
+Scaled_Normalized_Seurat_Object.RDS:
+	wget https://nextcloud.gustaveroussy.fr/s/p8Ab8Be43xFogYN/download/Scaled_Normalized_Seurat_Object.RDS
+
+ebaii:
+	mamba env create -p ./ebaii -f environment.yaml
+
+.PHONY:
+clean:
+	rm -rf ./ebaii *.RDS