Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence
Creators: name: Sopena-Rios, Maria
name: Ripoll-Cladellas, Aida
name: Omid, Fatemeh
name: Ballouz, Sara
name: Alquicira-Hernández, José
name: Oelen, Roy
name: Franke, Lude
name: van der Wijst, Monique
name: Powell, Joseph E.
name: Melé, Marta
Publisher: name: Zenodo
Year: 2024

description: Output data from "Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence": 



01_DEA_Results: Differential expression analysis with age 

02_Binomial_test_bias: Binomial test on the directionality of expression of differentially expressed genes with age 

03_DEA_sharing: Cell type sharing of genes differentially expressed with age 

04_DEA_Results_Replication_Oelen2022:  Differential expression analyses with age in the replication dataset form Oelen et al., 2022

05_CompositonalAnalysis_CellType: Cell type compositional analysis with age

06_CellCycleInfo_Seurat: Cell cycle phase scoring using Seurat 

07_CellCycleInfo_Tricycle: Cell cycle phase scoring using tricycle 

08_CompositionalAnalysis_CellCycle_Seurat:  Cell cycle phase compositional analysis with age form Seurat 

09_CompositionalAnalysis_CellCycle_Tricycle:  Cell cycle phase compositional analysis with age form Tricycle 

10_DifferentialEnrichment_Quiescence_AUCell: Differential enrichment analysis from quiescence gene set from AUCell 

11_DifferentialEnrichment_Senescence_AUCell: Differential enrichment analysis from senescence gene set from AUCell 

12_DifferentialEnrichment_Senescence_SenCID: Differential enrichment analysis from senescence gene set from SenCID 

13_CompostionalAnalysis_CellType_Replication_Oelen: Cell type compositional analysis with age in the replication dataset form Oelen et al., 2022

14_DEA_Results_Females: Differential expression analyses with age in females

15_DEA_Results_Males: Differential expression analyses with age in males

16_DEA_Results_Interaction: Differential expression analyses with the interaction of age:sex

17_CompositonalAnalysis_CellType_Females: Cell type compositional analysis with age in females

18_CompositonalAnalysis_CellType_Males: Cell type compositional analysis with age in males

19_CompositonalAnalysis_CellType_Interaction: Cell type compositional analysis with the interaction of age:sex

20_DifferentialAbundance_Females: Differential abundance analysis with age in females 

21_DifferentialAbundance_Males: Differential abundance analysis with age in females 

22_DifferentialAbundance_AllData_Subsampling1: Differential abundance analysis with age in a 25% random subsampling of the data 

23_DifferentialAbundance_AllData_Subsampling2: Differential abundance analysis with age in a 25% random subsampling of the data 

24_DifferentialAbundance_AllData_Subsampling3: Differential abundance analysis with age in a 25% random subsampling of the data 

25_Nhood-cell_id_Females: Correspondence of each individual cell to a Milo neighborhood in females 

26_Nhood-cell_id_Males: Correspondence of each individual cell to a Milo neighborhood in males 

27_Nhood_Markers: Markers of age-enriched or age-depeleted milo nhoods in males and females 

28_Enrichments_NhoodMarkers_Females: GO enrichments of markers from age-enriched neighborhoods in females

29_Enrichments_NhoodMarkers_Males: GO enrichments of markers from age-enriched neighborhoods in males

29_Enrichments_NhoodMarkers_Males: GO enrichments of markers from age-enriched neighborhoods in males

30_DEA_GZMB_Females: Differential expression analysis in CD8 TEM subpopulations in females 

30_DEA_GZMB_Males: Differential expression analysis in CD8 TEM subpopulations in males 

31_CompositonalAnalysis_CellType_GZMB_Females: Cell type compositional analysis with age for CD8 TEM subpopulations in females 

32_CompositonalAnalysis_CellType_GZMB_Males: Cell type compositional analysis with age for CD8 TEM subpopulations in males 

33_DEA_ISG_CD14_Mono_Females: Differential expression analysis with age in CD14 Mono subpopulations