Last updated: 2019-09-16
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Cell cycle phase and cell types - among many reasons - are argubly the most candidates driving differences in gene expression among cells.
peco is a supervised approach for predicting continuous cell cycle phase in single-cell RNA-seq (scRNA-seq) data analysis.
We developed peco in a study that combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs).
Our paper: Characterizing and inferring quantitative cell-cycle phase in single-cell RNA-seq data analysis.
Our software:
The development version can be downloaded from GitHub
devtools::install_github("jhsiao999/peco")
library(peco)GEO record GSE121265 for all raw and processed sequencing data
The processed data data sets are also available in as a gzip compressed tarball on the Gilad lab website: https://giladlab.uchicago.edu/wp-content/uploads/2019/02/Hsiao_et_al_2019.tar.gz.
All data sets used in our analysis are listed and downloadable at https://jdblischak.github.io/fucci-seq/data-overview.html.
Find out how we
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] 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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.4.0 Rcpp_1.0.2 digest_0.6.20 rprojroot_1.3-2
[5] backports_1.1.2 git2r_0.25.2 magrittr_1.5 evaluate_0.12
[9] highr_0.7 stringi_1.2.4 fs_1.3.1 whisker_0.3-2
[13] rmarkdown_1.10 tools_3.5.1 stringr_1.3.1 glue_1.3.0
[17] yaml_2.2.0 compiler_3.5.1 htmltools_0.3.6 knitr_1.20