Commit f5485961 authored by Giorgia Giacomini's avatar Giorgia Giacomini
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Update README.md

parent 70149e0c
...@@ -7,7 +7,7 @@ Amodio G, Giacomini G, Boeri L, et al. **T cell exhaustion and senescence signat ...@@ -7,7 +7,7 @@ Amodio G, Giacomini G, Boeri L, et al. **T cell exhaustion and senescence signat
scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/seurat/) pipeline that includes the following steps starting from a minimal object after loading of 10X data to markers identification: scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/seurat/) pipeline that includes the following steps starting from a minimal object after loading of 10X data to markers identification:
- Preprocessing and cell filtering - Preprocessing and cell filtering
- Each sample was pre-processed and cells with mitochondrial RNA percentages higher than 10 and a number of features <1200 or >6000, were filtered out. - Each sample was pre-processed and cells with mitochondrial RNA percentages higher than 10 and a number of features <1200 or >6000, were filtered out. Samples were merged into a single Seurat dataset
- Normalization - Normalization
- Default Seurat settings [(NormalizeData function)](https://satijalab.org/seurat/reference/normalizedata) - Default Seurat settings [(NormalizeData function)](https://satijalab.org/seurat/reference/normalizedata)
- Scaling: - Scaling:
...@@ -21,6 +21,8 @@ scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/ ...@@ -21,6 +21,8 @@ scRNAseq analysis was performed using a standard [Seurat](https://satijalab.org/
### Directories and Files ### ### Directories and Files ###
- sampleSheet.csv: names of samples and corresponding conditions
- **Script**: R scripts used for the analyses - **Script**: R scripts used for the analyses
- `1_PreProcessing_Data.R`: Preprocessing, cell filtering and Full object creation - `1_PreProcessing_Data.R`: Preprocessing, cell filtering and Full object creation
- `2_Infertility_scRNAseq_analysis.R`: - `2_Infertility_scRNAseq_analysis.R`:
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