LEAP: Constructing Gene Co-Expression Networks for Single-Cell RNA-Sequencing Data Using Pseudotime Ordering

Advances in sequencing technology now allow researchers to capture the expression profiles of individual cells. Several algorithms have been developed to attempt to account for these effects by determining a cell's so-called `pseudotime', or relative biological state of transition. By applying these algorithms to single-cell sequencing data, we can sort cells into their pseudotemporal ordering based on gene expression. LEAP (Lag-based Expression Association for Pseudotime-series) then applies a time-series inspired lag-based correlation analysis to reveal linearly dependent genetic associations.

AuthorAlicia T. Specht and Jun Li
Date of publication2016-09-13 21:19:05
MaintainerAlicia T. Specht <aspecht2@nd.edu>
LicenseGPL-2
Version0.2

View on CRAN

Files

LEAP
LEAP/inst
LEAP/inst/doc
LEAP/inst/doc/LEAP_Vignette.R
LEAP/inst/doc/LEAP_Vignette.Rnw
LEAP/inst/doc/lag_example.csv
LEAP/inst/doc/lag_My_name.csv
LEAP/inst/doc/MAC_symmetric_example.csv
LEAP/inst/doc/LEAP_Vignette.synctex.gz
LEAP/inst/doc/perm_example.csv
LEAP/inst/doc/LEAP_Vignette.pdf
LEAP/inst/doc/MAC_My_name.csv
LEAP/inst/doc/MAC_example.csv
LEAP/inst/doc/lag_symmetric_example.csv
LEAP/NAMESPACE
LEAP/data
LEAP/data/example_data.rda
LEAP/data/lag_example.RData
LEAP/data/perm_example.rda
LEAP/data/lag_example.rda
LEAP/data/example_data.RData
LEAP/data/MAC_example.RData
LEAP/data/MAC_example.rda
LEAP/data/perm_example.RData
LEAP/data/MAC_symmetric.RData
LEAP/data/MAC_symmetric.rda
LEAP/R
LEAP/R/MAC_lags.R LEAP/R/MAC_counter.R LEAP/R/MAC_perm.R
LEAP/vignettes
LEAP/vignettes/LEAP_Vignette.Rnw
LEAP/vignettes/lag_My_name.csv
LEAP/vignettes/MAC_My_name.csv
LEAP/MD5
LEAP/build
LEAP/build/vignette.rds
LEAP/build/partial.rdb
LEAP/DESCRIPTION
LEAP/man
LEAP/man/MAC_counter.Rd LEAP/man/MAC_symmetric.Rd LEAP/man/MAC_lags.Rd LEAP/man/lag_example.Rd LEAP/man/MAC_example.Rd LEAP/man/perm_example.Rd LEAP/man/example_data.Rd LEAP/man/LEAP-package.Rd LEAP/man/MAC_perm.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.