coolgenome / tcm

Codes used in pan-T cell analysis

T Cell Map

Codes used in pan-cancer T cell study

• "TCellMap.R" is a tool we developed to automatically align and annotate T cells in a scRNA-seq dataset. It uniformly aligns T cells from the query dataset with the T cell maps that we built in our pan-cancer T cell study.

• The python script "Res_largerT.py" functions as a pipeline for the analysis and visualization of SRT data.

• The directories titled "fig1/2/3/4/5/6" contain additional scripts used for generating figures in the manuscript. Furthermore, the "data_preprocess" folder hosts scripts designed to preprocess raw data. Those scripts are used for tasks such as batch-correction and dimensional reduction, etc.

tcm's Issues

subject ID missing

It appears that the individual subject IDs for each cell were not included in the Seurat object data that can be downloaded from the T cell map portal. My work would greatly benefit from capturing subject-level variation for statistical testing. For instance, according to Table S2 from the corresponding publication, there were samples from 11 individual cancer patients for the BCC data but there is insufficient data available in the Seurat objects to group cells by subjects.

If you are able, can you update the downloadable Seurat objects to include subject ID or provide the cell barcode-to-subject id mappings for the CD8+ and CD4+ data sets?

Seurat objects don't contain the raw count data

Hi,

Thank you for sharing the Seurat objects with us. I downloaded the Seurat objects for CD4 and CD8 T cells. However, the raw count data are missing. My understanding is that reverse normalization is not possible, and hence generating the count matrices from the normalized data is not possible. Unfortunately, some tools require the raw count data and don't function with normalized data. Would it be possible to acquire the raw count data?

Snapshots of the "count" and "data" slots:

snn-single-markers.tsv

hi，
How can I get the file snn-single-markers.tsv, is it possible to provide the file or can I replace it with the DEGtop50 from the article?
thanks！

Availability of reference Seurat objects

Hi,

Is the reference Seurat object available somewhere? I would like to run TCellMap.R.

refSeuratObj <- readRDS(opt$referenceData)