This repository contains the scripts used in the manuscript: Normal Breast Tissues Harbor Rare Populations of Aneuploid Epithelial Cells.
- Demultiplexed fastq files were first pre-processed by the pipeline: CNV_pipeline.
- Then R scripts in scDNA_analysis were used for downstream analysis and visualization.
- R scripts in stat_analysis were used for statistical testing and visualization.
- R scripts in ST_infer_CNAs were used for CNA inference in ST spots using CopyKat
Session info:
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_5.7 ggtree_3.2.1 ggpubr_0.4.0 magrittr_2.0.3
[5] BiocParallel_1.28.3 glue_1.6.2 forcats_1.0.0 stringr_1.5.0
[9] dplyr_1.1.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[13] tibble_3.1.8 ggplot2_3.4.1 tidyverse_1.3.1 copykit_0.1.2
[17] DNAcopy_1.68.0 Rsubread_2.8.2 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0
[21] Biobase_2.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[25] S4Vectors_0.32.4 BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.63.0
The original sequencing data from this study has been deposited to the Sequence Read Archive (SRA): PRJNA1003661.
For any additional information, please email corresponding author.