Merge pull request #73 from ARTbio/RNAseq-IOC-2

Work on IOC plan (9 weeks scheduled)

docs/bulk_RNAseq-IOC/01_IOC_RNAseq.md

@@ -1,55 +1,79 @@
-##  Introduction to the IOC ARTbio 064: Bulk RNAseq Analyses
+#  Introduction to the IOC ARTbio 064: Bulk RNAseq Analyses
 **November 2023**
 
 In this Interactive Online Companionship, we will train to perform RNAseq analyses
 of Bulk RNAseq
 
-### Program / Schedule
-
-### Week 1
-
-  **3-hours Zoom video-conference with**
-
-  1. Introduction of the Companions and Instructors (10 min)
-  - Presentation of the IOC general workflow (Scheme) (15 min)
-  - Presentation of the IOC tools (2 hours)
-      1. Zoom (5 min)
-      - Starbio (5 min)
-      - Slack (10 min)
-      - GitHub (20 min)
-      - Psilo storage (15 min)
-      - Galaxy (65 min)
-<!-- Ici on est à 2:25, faire un schedule sur google sheets -->
-<ol start=4>
-  <li> Import data from Psilo to Galaxy
-  <li> Program of the week 2
-  <ol start="a">
-    <li> Presentation of exercises with digital tools
-    <li> presentation of pretreatment and metadata organisations and of related tasks to be done
-  </ol>
-</ol>
-
-### Week 2
-1. Question on Week 2
+## Program / Schedule
+
+### Week 1 - **3-hours Zoom video-conference**
+<!-- Faire un schedule sur google sheets -->
+
+1. Introduction of the Companions and Instructors (10 min)
+- Presentation of the IOC general workflow (Scheme) (15 min)
+- Presentation of the IOC tools (2 hours)
+    1. Zoom (5 min)
+    - Starbio (5 min)
+    - Slack (10 min)
+    - GitHub (20 min)
+    - Psilo storage (15 min)
+    - Galaxy (65 min)
+    - Import data from Psilo to Galaxy
+- Work Program of the week 1 - [Week-1 exercises]()
+    1. Exercises with Slack (use of markdown, configuration, files, no-screen-shots, etc.)
+    - Exercises with GitHub (web version)
+    - Data upload in Galaxy, from Psilo
+    - Pretreatment (renaming and collections) and metadata organisations (and basic Galaxy manipulation)
+
+### Week 2 - **Quality control and References**
+1. Question on Week 1
     1. Data upload
-    2. Quality control
-- Program of Week 3
-    1. reference datasets (GTF, genome, subset, ucsc tables, ensembl Biomart)
-### Week 3
-2. Questions on Week 2
+    2. Renaming, metadata organisation, collections
+    3. Check point of data availability in Galaxy accounts
+- Program of Week 2 - [Week-2 exercices]()
+    1. Quality control (fastqc, multiQC, adapter trimming)
+    2. reference datasets (Genome, GTF, subsets, ucsc tables, ensembl Biomart)
+### Week 3 - **Read Mapping and Bam manipulation**
+1. Questions on Week 2
     1. reference
     - GTF manipulation
-- Program of the Week 3
+    - production of two parallel datasets, filtered/trimmed and not preatreated
+- Program of the Week 3 [Week-3 exercices]()
     1. Mapping and mappers
     2. Inspection of Bam files
+    - InferExperiment for read orientations
+
+### Week 4 - **Counting Reads or Fragments**
+1. Questions on Week 3
+- Program of the Week 4 [Week-4 exercices]()
+    1. FeatureCount
+    2. HTSeq-counts
+    3. Count statistics and visualisations (side by side Scratchbook, R, etc)
+
+### Week 5 - **Statistical Analysis of Differential Gene Expression**
+1. Questions on Week 4
+- Program of the Week 5 [Week-5 exercices]()
+    1. DESeq2
+    - EdgeR
+    - Volcano Plots, Waterfall plots
+    - RUVseq
+
+### Week 6 - **Gene Enrichment Analysis**
+1. Questions on Week 5
+- Program of the Week 6 [Week-6 exercices]()
+    1. GOseq
+
+
+### Week 7 - **Gene Set Enrichment Analyses (GSEA)**
+1. Questions on Week 6
+- Program of the Week 7 [Week-7 exercices]()
+    1. GSEA
 
-3. Analysis of the differential gene expression
-    1. Count the number of reads per annotated gene
-    2. Viewing datasets side by side using the Scratchbook
-    3. Identification of the differentially expressed features
-    4. Visualization of the differentially expressed genes
-    5. Analysis of functional enrichment among the differentially expressed genes
+### Week 8 - **Galaxy Workflows**
+1. Questions on Week 7
+- Program of the Week 8 [Week-5 exercices]()
+    1. building clean workflows to capture all details of the analysis
 
-Some parts of this IOC were inspired by
-[Reference-based RNAseq analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html)
-of the Galaxy Training Network (GTN)
+### Week 9 - **Presentations of the analyses by the companions**
+1. Questions on Week 8 (30 min max)
+- 20 min presentations by the attendees

docs/bulk_RNAseq-IOC/links.md

@@ -0,0 +1,5 @@
+# External References
+
+- This IOC program was inspired by
+  [Reference-based RNAseq analysis](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html)
+  of the Galaxy Training Network (GTN)

mkdocs.yml

@@ -173,7 +173,8 @@ nav:
         - References: scRNAseq_basics/references.md
 
     - IOC on bulk RNAseq analysis:
-        - Introductive Session: bulk_RNAseq-IOC/01_IOC_RNAseq.md
+        - Introduction - Week-1: bulk_RNAseq-IOC/01_IOC_RNAseq.md
+        - External Materials: bulk_RNAseq-IOC/links.md
     -  Introduction to Deep-seq Analysis:
         - INTRODUCTION: deepseq/index.md
         - Illumina sequencing: deepseq/illumina.md