Update

.gitattributes

 **/dataset/** filter=lfs diff=lfs merge=lfs -text
+/runs/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text

README.md

 # ARC mininmal Example RNASeq
 
-This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations. 
+This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations.
 
 ## Data origin
-- Partly published under: https://doi.org/10.1104/pp.15.01076
-- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details. 
+
+- Partly published under: <https://doi.org/10.1104/pp.15.01076>
+- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details.
 
 ## Additional payload
+
 > The following folders are not part of the ARC  
 > for details, see: [ARC specs:Additional paylod](https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#additional-payload)
 
@@ -14,34 +16,33 @@ Directory | Purpose
 ---- | ----
 [_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO
 
-
 ## Notes and ToDos
 
 ### Experimental metadata in isa.assay.xlsx
-- split GEO SWATE templates into four sheets 
-    - 1SPL01_plants
-    - 2EXT01_RNA
-    - 3ASY01_RNASeq
-    - 4COM01_RNASeq
 
-### Adding large raw data via git lfs 
+- split GEO SWATE templates into four sheets
+  - 1SPL01_plants
+  - 2EXT01_RNA
+  - 3ASY01_RNASeq
+  - 4COM01_RNASeq
 
-1. Before addind the files to the ARC, track them via `git lfs`
-
-```
-git lfs track "*.fastq.gz"
-git lfs track "01_kallisto_index"
+### Adding large raw data via git lfs
 
-```
+1. Before addind the files to the ARC, track them via `git lfs`
 
-2. Move / add the large data files to the respective folders
+    ```bash
+    git lfs track "*.fastq.gz"
+    git lfs track "01_kallisto_index"    
+    ```
 
-3. Add them via `git add`
+1. Move / add the large data files to the respective folders
 
-```
-git add assays/Talinum_RNASeq_minimal/dataset/
-git add runs/run1/01_kallisto_index
+1. Add them via `git add`
 
-```
+    ```bash
+    git add assays/Talinum_RNASeq_minimal/dataset/
+    git add runs/run1/01_kallisto_index
+    
+    ```
 
-4. Commit
+1. Commit

workflows/.Rhistory

+ARC_root="~/03_DataPLANT_gitlab/samplearc_rnaseq/"

workflows/06_plot_shinyApp.Rmd

@@ -14,7 +14,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 # Load data
 
-ARC_root="~/Hackathon_ARCexample_rnaseq/"
+ARC_root="~/03_DataPLANT_gitlab/samplearc_rnaseq/"
 load(file = paste0(ARC_root, 'runs/05_shinyPrep.RData'))
 
 ```