LINC: co-expression of lincRNAs and protein-coding genes

This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the 'Guilty by Association' approach.

Author
Manuel Goepferich, Carl Herrmann
Date of publication
None
Maintainer
Manuel Goepferich <manuel.goepferich@gmx.de>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

Man pages

Arith-methods
Plus Operator '+' In 'LINC'
assignment-methods
Methods for the Getter Function 'assignment' in Package...
BRAIN_EXPR
mRNA Expression Of Normal BRAIN From GTEX And TCGA
changeOrgDb
Change the Gene Annotation / Model Organism
clusterlinc-methods
Cluster Queried ncRNAs Based On Their Interaction Partners
correlation-methods
Methods for the Getter Function 'correlation' in Package...
express-methods
Methods for the Getter Function 'express' in Package 'LINC'
feature
Manipulate Objects Of The 'LINC' class
getbio-methods
Find Enriched Biological Terms For A Cluster
getcoexpr
Get IDs For Co-Expressed Genes from The 'LINC' Class
getlinc-methods
Subsetting for 'LINC' objects
history-methods
Methods for the Getter Function 'history' in Package 'LINC'
justlinc-methods
Co-Expression Analysis Of ncRNA Genes In One Step
LINCbio-class
Class '"LINCbio"'
LINCcluster-class
Class '"LINCcluster"'
linCenvir-methods
Methods for the Getter Function 'linCenvir' in Package 'LINC'
LINCfeature-class
Class '"LINCfeature"'
LINCmatrix-class
Class '"LINCmatrix"'
linc-methods
Compute A Correlation Matrix of Co-expressed Coding And...
LINCsingle-class
Class '"LINCsingle"'
linctable-methods
Write To Table 'LINC'
plotlinc-methods
Plot Objects Of The 'LINC' class
querycluster
Cluster One ncRNA Gene Based On Its Co-Expression in Multiple...
results-methods
Methods for the Getter Function 'results' in Package 'LINC'
singlelinc-methods
Co-Expression Analysis Of A Single ncRNA Gene

Files in this package

LINC/DESCRIPTION
LINC/NAMESPACE
LINC/NEWS
LINC/R
LINC/R/LINC_CLASSES.R
LINC/R/LINC_FUNCTIONS.R
LINC/R/LINC_METHODS.R
LINC/R/RcppExports.R
LINC/R/sysdata.rda
LINC/build
LINC/build/vignette.rds
LINC/data
LINC/data/BRAIN_EXPR.RData
LINC/inst
LINC/inst/doc
LINC/inst/doc/LINC.R
LINC/inst/doc/LINC.Rmd
LINC/inst/doc/LINC.html
LINC/inst/extdata
LINC/inst/extdata/barplot_img.png
LINC/inst/extdata/clust_img.png
LINC/inst/extdata/overview_img.png
LINC/inst/extdata/querycluster_img.png
LINC/inst/extdata/singlelinc_img.png
LINC/inst/extdata/statslinc_img.png
LINC/inst/extdata/stclust_img.png
LINC/inst/unitTests
LINC/inst/unitTests/test_LINC.R
LINC/man
LINC/man/Arith-methods.Rd
LINC/man/BRAIN_EXPR.Rd
LINC/man/LINCbio-class.Rd
LINC/man/LINCcluster-class.Rd
LINC/man/LINCfeature-class.Rd
LINC/man/LINCmatrix-class.Rd
LINC/man/LINCsingle-class.Rd
LINC/man/assignment-methods.Rd
LINC/man/changeOrgDb.Rd
LINC/man/clusterlinc-methods.Rd
LINC/man/correlation-methods.Rd
LINC/man/express-methods.Rd
LINC/man/feature.Rd
LINC/man/getbio-methods.Rd
LINC/man/getcoexpr.Rd
LINC/man/getlinc-methods.Rd
LINC/man/history-methods.Rd
LINC/man/justlinc-methods.Rd
LINC/man/linCenvir-methods.Rd
LINC/man/linc-methods.Rd
LINC/man/linctable-methods.Rd
LINC/man/plotlinc-methods.Rd
LINC/man/querycluster.Rd
LINC/man/results-methods.Rd
LINC/man/singlelinc-methods.Rd
LINC/src
LINC/src/Cppspear.cpp
LINC/src/LINC_init.c
LINC/src/RcppExports.cpp
LINC/src/docdd.cpp
LINC/src/doesd.cpp
LINC/tests
LINC/tests/runTests.R
LINC/vignettes
LINC/vignettes/LINC.Rmd