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

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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.

Author
Alicia T. Specht and Jun Li
Date of publication
2016-09-13 21:19:05
Maintainer
Alicia T. Specht <aspecht2@nd.edu>
License
GPL-2
Version
0.2

View on CRAN

Man pages

example_data
Numeric data frame of example data
lag_example
Integer data frame
LEAP-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("LEAP")}
MAC_counter
Function to perform lag-based correlation anaylsis of...
MAC_example
Numerical matrix
MAC_lags
Internal function used by MAC_counter and MAC_perm
MAC_perm
Function to perform a permutation analysis to determine a...
MAC_symmetric
Numeric data frame
perm_example
The resulting data ouptut from applying MAC_perm() to...

Files in this package

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