KMT2A-r Leukemia Paper

Descroption of R codes used in generating manuscript "Single-cell multiomics reveals increased plasticity, resistant populations and stem-cell-like blasts in KMT2A-rearranged leukemia". The codes are organized into the following categories:

Process/integrate scRNA-Seq data

• script_process_scRNA_single_sample.R -- process each sample from cellranger output
• integrate_18MLLr_scRNA.R -- integrate scRNA-Seq data for all patient samples
• integrate_hd_scRNA.R -- integrate scRNA-Seq data for all healthy donor samples
• integrate_18MLLr_scRNA_normalCells.R -- integrate normal cells from scRNA-Seq data for all patient samples

Process/integrate scATAC-Seq data

• integrate_18MLLr_scATAC.R -- integrate scRNA-Seq data for all patient samples
• integrate_hd_scATAC.R -- integrate scATAC-Seq data for all healthy donor samples
• integrate_18MLLr_scATAC_normalCells.R -- integrate normal cells from scATAC-Seq data for all patient samples

Label transfering

• transfer_lable.R -- Label transfering form scRNA-Seq data to scATAC-Seq data to annotate HD scATAC-Seq data

Projection

• project2norm_rna.R. -- project patient cells on top of umap of normal reference (HD) using scRNA-Seq data
• project2norm_atac.R -- project patient cells on top of umap of normal reference (HD) using scATAC-Seq data

TF enrichment analysis

• script_chromVAR_allPeaks.R -- run chromVAR given a seurat object
• compTFenrich_18MLLr.R -- comparing TF enrichment between different groups using saved chromVAR outputs/objects

Analysis of snmC-Seq2 data

• integrate_snmc.R -- integrate all snmc-seq2 data
• coembedding_snmc.R -- coembedding snmc-seq2 with corresponding scATAC-Seq data
• pseudo_bulk_snmc.R -- compare differential methylated regions between young vs old group by developmental stage

Cell-Cell-Communication analysis

• prepInputs4CellphoneDB.R -- prepare inputs for running cellphoneDB
• compare_cell_interactions_HSPC1vsBlasts.R -- compare ligand-receptor pairs between HSPC1vsImmune and BlastvsImmnue

Lineage switch analysis

• lineage_swithc_example.R -- analysis of 2 patients whose leukemia underwent lineage switch upon treatment
• lineage_switch_analysis_updated.R -- overall analysis of lineage switch

EP prediction and TRN analysis

• regr_ep_prediction_general.R -- predict E-P interactions using linear regression
• construct_netweor_HSPC1_updown.R -- construct TRN for HSPC-like population

Long read analysis

• filter_alignqc_res.R -- filter alignqc result for downstream use
• sum_longread_final.R --- summarize detection rate using longGF & alignqc overlapped result

Reference

Chen, C., Yu, W., Alikarami, F., Qiu, Q., Chen, C. H., Flournoy, J., ... & Tan, K. (2020). Single-cell multiomics reveals increased plasticity, resistant populations and stem-cell-like blasts in KMT2A-rearranged leukemia