Short form Full name
BCCBasal cell carcinoma
BRCABreast Cancer
CBTChildhood Brain Tumor
CESCCervical Cancer
CRCColorectal Cancer
CSCCCutaneous Squamous Cell Carcinoma
GBMGlioblastoma
GISTGastrointestinal Stromal Tumor
HGSOCHigh-grade Serous Ovarian Cancer
LIHCLiver Hepatocellular Carcinoma
LUADLung Adenocarcinoma
MIBCMuscle-invasive Bladder Cancer
OVOvarian Carcinoma
PCNSLPrimary Central Nervous System Lymphoma
PDACPancreatic Ductal Adenocarcinoma
PRADProstate Cancer
RCCRenal Cell Carcinoma
SKCMMelanoma

Short form Full name
B-LymB lymphocyte
Plasmaplasma cell
B-Nainaive B cell
B-Regregulatory B cell
B-Memmemory B cell
B-Folfollicular B cell
GC Bgerminal center B cell
GC B-DZgerminal center B cell in the dark zone
GC B-LZgerminal center B cell in the light zone
NKnatural killer cell
T-LymT lymphocyte
T-Nainaive T cell
T-Proproliferative T cell
T-TRMtissue-resident memory T cell
T-EMeffect memory T cell
NKTnatural killer T cell
T-gdgamma delta T cell
CD4+ TCD4+ T cell
CD4+ T-Nainaive CD4+ T cell
CD4+ T-Memmemory CD4+ T cell
Th1T helper type 1 cell
Th2T helper type 2 cell
Th17T helper type 17 cell
T-FHfollicular T helper cell
T-Regregulatory T cell
CD8+ TCD8+ T cell
CD8+ T-Nainaive CD8+ T cell
T-Cytcytotoxic T cell
CD8+ T-Effeffector CD8+ T cell
CD8+ T-Memmemory CD8+ T cell
T-Exhexhausted T cell
Myeloidmyeloid cell
Monocytemonocyte
Macrophagemacrophage
Mac-M1M1-type macrophage
Mac-M2M2-type macrophage
DCdendritic cell
cDC1conventional type 1 dendritic cell
cDC2conventional type 2 dendritic cell
aDCactive dendritic cell
pDCplasmacytoid dendritic cell
Neutrophilsneutrophil
MASTmast cell
Progenitorprogenitor
Erythroiderythroid
Cyclingcycling cell
Pre-Bprecursor B cell
Pro-Bprogenitor B cell
GC B-IGC B-I
GC B-IIGC B-II
Plasmablastsplasmablast
ABCage-associated B cell
NK-CD16+CD16+ natural killer cell
NK-CD56bright-CD16-CD56bright CD16- natural killer cell
T&NK-CycCycling T&natural killer cell
T-CD4;CD8CD4+ T cell;CD8+ T cell
T-Eff;EM-CD4effector T cell;effect memory CD4+ T cell
T-EM;EMRA-CD8effect memory T cell;EMRA CD8+ T cell
T-Nai;CM-CD4naive T cell;center memory CD4+ T cell
T-Nai;CM-CD4-Actnaive T cell;activated center memory CD4+ T cell
T-Nai;CM-CD8naive T cell;center memory CD8+ T cell
T-RM;EM-CD8tissue-resident memory T cell;effect memory CD8+ T cell
TRM-gut-CD8tissue-resident memory_gut_CD8 T cell
TRM-Tgdtissue-resident memory_gamma delta T cell
TRM-Th1;Th17tissue-resident memory_T helper type 1 cell;T helper type 17 cell
Tgd-CRTAM+CRTAM+ gamma delta T cell
MAITmucosal associated invariant T cell
T;BT lymphocyte;B lymphocyte
MNP;BMNP;B lymphocyte
MNP;TMNP;T lymphocyte
Megakaryocytesmegakaryocyte
Mon-Clsclassical monocyte
Mon-nonClsnon-classical monocyte
Mac-Eryerythrophagocytic macrophage
Mac-Alvalveolar macrophage
Mac-IntMedintermediate macrophage
Mac-Intintestinal macrophage
DC1conventional type 1 dendritic cell
DC2conventional type 2 dendritic cell
migDCmigratory dendritic cell
ILC3type 3 innate lymphoid cell

Method Description Reference
RCTDSpatial spot deconvolution 1
SVGIdentifying high spatial variability genes 2
Co-occurrenceIdentifying tumor Co-occurrenced immune cells3
COSGIdentifying cell types/clusters marker genes 4
ITALKIdentifying interactions between cell types 5

1 : Cable, D., Murray, E., Zou, L., Goeva, A., Macosko, E., Chen, F., and Irizarry, R. (2022). Robust decomposition of cell type mixtures in spatial transcriptomics. Nature biotechnology 40, 517-526.

2 : Edsgard, D., Johnsson, P., and Sandberg, R. (2018). Identification of spatial expression trends in single-cell gene expression data. Nature methods 15, 339-342.

3 : Khamis, D., Fowler, D., Morrissey, E., et al. (2021). Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184, 810-826.e823.

4 : Dai, M., Pei, X., and Wang, X. (2022). Accurate and fast cell marker gene identification with COSG. Briefings in bioinformatics 23.

5 : Wang, Y., Wang, R., et al. (2019). iTALK: an R Package to Characterize and Illustrate Intercellular Communication. bioRxiv [Preprint]