This repository contains matadata and codes necessary for analysis of the scRNA and scBCR data of human LUAD presented in Hao et al. Cancer Discovery, in revision (2022).
Cells with low complexity libraries or likely cell debris have been removed. Batch effect was corrected by Harmony and verified by k-BET. The Change-O repertoire clonal assignment toolkit was used to define B cell clones.
Please contact LWang22@mdanderson.org and hkadara@mdanderson.org with any questions.
cell2subtype and cell2BCR_clone have been organized into R objects that can be downloaded from /Input_data/.
Cell level metadata is available in the provided /Input_data/Cell metaData.rda, which contains QC statistics of cells, clinical information of associated samples and cell types.
Cell level BCR clones and SHM are available in the provided /Input_data/10Xclone_mutation.rda, which contains all the required BCR data of each cell, including VDJ calls, clones, SHM and associated information of corresponding samples.
Cell_ID to cell type association for all the TME cells are available in the provided /input_data/cellType_All.rda.
All the raw data are uploading to EGA at the moment and the accession number will be released very soon (2022-07-27).
Tested on macOS Big Sur
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R version: 4.1.2
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R packages
- ggplot2
- data.table
- Seurat
- dplyr
- tidyr
- ggpubr
- RColorBrewer
- monocle
- smoother
- pheatmap
- Hmisc
- monocle3
- ggrepel
- CytoTRACE
- shazam
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igblast_1.17.1
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Change-O toolkit