SiniscalcoTFR

Analysis of public scRNA-Seq data to identify TFR

Analysis of Gribonika I et al. (2022) dataset

code:

• preprocessing: [MD]

input:

• Cellranger H5 files: [DIR]
• Sample annotation: [TSV]

output:

• Seurat object will all cells: (data release) e-mtab-11805.seuratObj.RData
• Seurat object with unstimulated T cells: (data release) tcellObj.cca.RData
• Seurat object with unstimulated Foxp3 expressing cells (with Treg vs Tfr annotation): [RDA]
• Seurat object with stimulated T cells: (data release) stimObj.cca.RData
• Seurat object with stimulated Foxp3 expressing cells (with Treg vs Tfr annotation): [RDA]
• DEGs stim versus unstim in Tregs: [CSV]
• DEGs stim versus unstim in Tfrs: [CSV]

Analysis of Le Cox C. et al. (2023) dataset

code:

• preprocessing: [MD]

input:

• Cellranger MTX files: (data release)

output:

• Seurat object will all cells: (data release) gse214572.seuratObj.RData
• DEG between Treg and Tfrs: [CSV]