Last updated: 2020-10-03
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Knit directory: peco-paper/
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peco is a supervised approach for predicting continuous cell cycle phase using single-cell RNA-seq (scRNA-seq) data. The approach is described in our paper.
We use this site to document and share the code used to produce our analysis. Please feel free to explore. Comments and feedbacks are welcome!
We quantified continous cell cycle phase using FUCCI fluorescence imaging and trained peco to predict this continuous cell cycle phase using scRNA-seq data collected from six human cell lines. Our paper showed that peco produces robust cell cycle phase predictions using strong cyclic genes - genes which expression levels oscillate along the cell cycle.
The software peco will be released in Biconductor 3.11. This release will use the latest R3.6.1.
The development version is available on GitHub. To install the development version,
devtools::install_github("jhsiao999/peco")
library(peco)Characterizing and inferring quantitative cell-cycle phase in single-cell RNA-seq data analysis.
You have two main options for downloading the data files. First, you can manually download the individual files by clicking on the links on this page or navigating to the files in the peco-paper GitHub repository. This is the recommended strategy if you only need a few data files.
Second, you can install git-lfs. To handle large files, we used Git Large File Storage (LFS). This means that the files that you download with git clone are only plain text files that contain identifiers for the files saved on GitHub's servers. If you want to download all of the data files at once, you can do this with after you install git-lfs.
To install git-lfs, follow their instructions to download, install, and setup (git lfs install). Alternatively, if you use conda, you can install git-lfs with conda install -c conda-forge git-lfs. Once installed, you can download the latest version of the data files with git lfs pull.
GEO record GSE121265 for all raw and processed sequencing data.
We also provide the processed data in TXT format as a gzip compressed tarball on the Gilad lab website.
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 whisker_0.4 knitr_1.30 magrittr_1.5
[5] R6_2.4.1 rlang_0.4.7 stringr_1.4.0 tools_3.6.3
[9] xfun_0.17 git2r_0.27.1 htmltools_0.5.0 ellipsis_0.3.1
[13] yaml_2.2.1 digest_0.6.25 rprojroot_1.2 tibble_3.0.3
[17] lifecycle_0.2.0 crayon_1.3.4 later_1.1.0.1 vctrs_0.3.4
[21] promises_1.1.1 fs_1.5.0 glue_1.4.2 evaluate_0.14
[25] rmarkdown_2.3 stringi_1.5.3 compiler_3.6.3 pillar_1.4.6
[29] backports_1.1.10 httpuv_1.5.4 pkgconfig_2.0.3