| Antibodies |
|
| Anti-CD3 antibody |
Abcam |
Cat# ab16669, RRID: AB_443425
|
| Anti-CD8 antibody |
Abcam |
Cat# ab93278, RRID: AB_10563532
|
| Goat Anti-Rabbit IgG |
Abbkine |
Cat# A21020, RRID: AB_2876889
|
|
| Deposited data |
|
| RNA-seq, genomic data and clinical data for the TCGA cohort |
TCGA |
https://xenabrowser.net/datapages |
| The TCR diversity profiling data |
Bagaev et al. study |
https://doi.org/10.1016/j.ccell.2021.04.014 |
| GSE135222 |
Gene Expression Omnibus (GEO) |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135222 |
| GSE126044 |
Gene Expression Omnibus (GEO) |
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126044 |
| IMvigor210 |
IMvigor210 |
http://research-pub.gene.com/IMvigor210CoreBiologies |
| OAK and POPLAR cohort |
EGAS00001005013 |
https://ega-archive.org/datasets/EGAD00001007703 |
| NFH cohort |
HRA003748 |
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA003748 |
| Kim et al. cohort |
PRJEB25780 |
https://www.ebi.ac.uk/ena/browser/view/PRJEB25780 |
|
| Software and algorithms |
|
| R version 4.1.1 |
R project |
https://www.r-project.org/ |
| IOBR |
Github |
https://github.com/IOBR/IOBR |
| KOBAS-I |
KOBAS-I |
http://kobas.cbi.pku.edu.cn/kobas3 |
| IKCscore |
Github |
https://github.com/LiaoWJLab/IKCscore |
| DESeq2 version 1.36.0 |
Github |
https://github.com/mikelove/DESeq2 |
| Maftools 2.8.0 |
Github |
https://github.com/PoisonAlien/maftools |
| CIBERSORT |
CIBERSORT |
https://cibersort.stanford.edu/ |
| GSVA version 1.40.1 |
Github |
https://github.com/rcastelo/GSVA |
