LINC: co-expression of lincRNAs and protein-coding genes
Version 1.4.0

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.

AuthorManuel Goepferich, Carl Herrmann
Bioconductor views BiologicalQuestion GeneExpression GeneRegulation Software
Date of publicationNone
MaintainerManuel Goepferich <manuel.goepferich@gmx.de>
LicenseArtistic-2.0
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("LINC")

Getting started

README.md
*LINC* - Co-Expression Analysis of lincRNAs

Popular 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
feature: Manipulate Objects Of The 'LINC' class
getbio-methods: Find Enriched Biological Terms For A Cluster
linc-methods: Compute A Correlation Matrix of Co-expressed Coding And...
See all...

All man pages Function index File listing

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

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/LINC_CLASSES.R
R/LINC_FUNCTIONS.R
R/LINC_METHODS.R
R/RcppExports.R
R/sysdata.rda
README.md
build
build/vignette.rds
data
data/BRAIN_EXPR.RData
inst
inst/doc
inst/doc/LINC.R
inst/doc/LINC.Rmd
inst/doc/LINC.html
inst/extdata
inst/extdata/barplot_img.png
inst/extdata/clust_img.png
inst/extdata/overview_img.png
inst/extdata/querycluster_img.png
inst/extdata/singlelinc_img.png
inst/extdata/statslinc_img.png
inst/extdata/stclust_img.png
inst/unitTests
inst/unitTests/test_LINC.R
man
man/Arith-methods.Rd
man/BRAIN_EXPR.Rd
man/LINCbio-class.Rd
man/LINCcluster-class.Rd
man/LINCfeature-class.Rd
man/LINCmatrix-class.Rd
man/LINCsingle-class.Rd
man/assignment-methods.Rd
man/changeOrgDb.Rd
man/clusterlinc-methods.Rd
man/correlation-methods.Rd
man/express-methods.Rd
man/feature.Rd
man/getbio-methods.Rd
man/getcoexpr.Rd
man/getlinc-methods.Rd
man/history-methods.Rd
man/justlinc-methods.Rd
man/linCenvir-methods.Rd
man/linc-methods.Rd
man/linctable-methods.Rd
man/plotlinc-methods.Rd
man/querycluster.Rd
man/results-methods.Rd
man/singlelinc-methods.Rd
src
src/Cppspear.cpp
src/LINC_init.c
src/RcppExports.cpp
src/docdd.cpp
src/doesd.cpp
tests
tests/runTests.R
vignettes
vignettes/LINC.Rmd
LINC documentation built on May 20, 2017, 10:26 p.m.

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