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.

AuthorManuel Goepferich, Carl Herrmann
Date of publicationNone
MaintainerManuel Goepferich <manuel.goepferich@gmx.de>
LicenseArtistic-2.0
Version1.2.0

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

Functions

+ Man page
Arith Man page
assignment Man page
assignment,LINCbio-method Man page
assignment,LINCcluster-method Man page
assignment,LINCmatrix-method Man page
assignment,LINCsingle-method Man page
assignment-methods Man page
BRAIN_EXPR Man page
cerebellum Man page
changeOrgDb Man page
clusterlinc Man page
clusterlinc,LINCcluster-method Man page
clusterlinc,LINCmatrix-method Man page
clusterlinc-methods Man page
correlation Man page
correlation,LINCbio-method Man page
correlation,LINCcluster-method Man page
correlation,LINCmatrix-method Man page
correlation,LINCsingle-method Man page
correlation-methods Man page
cortex Man page
crbl_cc Man page
crbl_cluster Man page
crbl_matrix Man page
ctx_cc Man page
ctx_cluster Man page
express Man page
express,LINCbio-method Man page
express,LINCcluster-method Man page
express,LINCmatrix-method Man page
express,LINCsingle-method Man page
express-methods Man page
feature Man page
gbm_cluster Man page
getbio Man page
getbio,LINCcluster-method Man page
getbio-methods Man page
getcoexpr Man page
getlinc Man page
getlinc,ANY,character-method Man page
getlinc-methods Man page
glioblastoma Man page
hippocampus Man page
history Man page
history,LINCbio-method Man page
history,LINCcluster-method Man page
history,LINCmatrix-method Man page
history,LINCsingle-method Man page
history-methods Man page
hpc_cluster Man page
justlinc Man page
justlinc,matrix-method Man page
justlinc-methods Man page
linc Man page
LINCbio-class Man page
+,LINCbio,LINCfeature-method Man page
LINCcluster-class Man page
+,LINCcluster,LINCfeature-method Man page
linc,data.frame,ANY-method Man page
linCenvir Man page
linCenvir,LINCbio-method Man page
linCenvir,LINCcluster-method Man page
linCenvir,LINCmatrix-method Man page
linCenvir,LINCsingle-method Man page
linCenvir-methods Man page
linc,ExpressionSet,ANY-method Man page
LINCfeature-class Man page
linc,LINCmatrix,missing-method Man page
linc,matrix,ANY-method Man page
LINCmatrix-class Man page
+,LINCmatrix,LINCfeature-method Man page
linc-methods Man page
LINCsingle-class Man page
linctable Man page
linctable,character,LINCcluster-method Man page
linctable-methods Man page
+-methods Man page
pcgenes_crbl Man page
pcgenes_ctx Man page
pcgenes_gbm Man page
pcgenes_hpc Man page
plotlinc Man page
plotlinc,LINCbio,character-method Man page
plotlinc,LINCbio,missing-method Man page
plotlinc,LINCcluster,character-method Man page
plotlinc,LINCcluster,missing-method Man page
plotlinc,LINCmatrix,character-method Man page
plotlinc,LINCmatrix,missing-method Man page
plotlinc,LINCsingle,character-method Man page
plotlinc,LINCsingle,missing-method Man page
plotlinc-methods Man page
querycluster Man page
results Man page
results,LINCbio-method Man page
results,LINCcluster-method Man page
results,LINCmatrix-method Man page
results,LINCsingle-method Man page
results-methods Man page
singlelinc Man page
singlelinc,LINCmatrix-method Man page
singlelinc-methods Man page

Files

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

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