A B C D E G I L M N O P R S T U misc
%*%-method | Class "namedSparse" adds margin names to sparse matrices |
%+% | Class "namedSparse" adds margin names to sparse matrices |
+-method | Class "namedSparse" adds margin names to sparse matrices |
A.csr | ~~data-name / kind ... |
accessMat | matrix utilities for ontoTools. |
accessMat-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
adjMat | Class "compoundGraph" list representation of multiple graph::graph |
adjMat-method | Class "compoundGraph" list representation of multiple graph::graph |
AMN | Class "namedSparse" adds margin names to sparse matrices |
annoSource-class | Vocabulary for genomic data integration |
annotationResource-class | Vocabulary for genomic data integration |
Arith-method | Class "namedSparse" adds margin names to sparse matrices |
as.matrix-method | Class "namedSparse" adds margin names to sparse matrices |
as.matrix.ok | Class "namedSparse" adds margin names to sparse matrices |
between | Class "compoundGraph" list representation of multiple graph::graph |
between-method | Class "compoundGraph" list representation of multiple graph::graph |
buildGOgraph | build graphNEL corresponding to bioc GO environment |
child2parentMatDense | matrix utilities for ontoTools. |
child2parentMatSparse | matrix utilities for ontoTools. |
children | Structures for working with formal nomenclatures |
children-method | Class "taggedHierNomenclature" ~~~ |
colinds | Class "namedSparse" adds margin names to sparse matrices |
colinds-method | Class "namedSparse" adds margin names to sparse matrices |
colSums | Class "namedSparse" adds margin names to sparse matrices |
colSums-method | Class "namedSparse" adds margin names to sparse matrices |
colSumsSp | Class "namedSparse" adds margin names to sparse matrices |
compoundGraph-class | Class "compoundGraph" list representation of multiple graph::graph |
conceptProbs | Compute semantic similarity measure for terms in an object-ontology |
coverageMat | Class "OOC" object-ontology complex |
coverageMat-method | Class "OOC" object-ontology complex |
coverMat | matrix utilities for ontoTools. |
DAG | Class "rootedDAG" |
DAG-method | Class "rootedDAG" |
daughterMat | matrix utilities for ontoTools. |
daughterSpMat | matrix utilities for ontoTools. |
depthStruct | tools for manipulating depth concepts for rooted DAGs |
dimnames-method | Class "namedSparse" adds margin names to sparse matrices |
dimnames<--method | Class "namedSparse" adds margin names to sparse matrices |
DMdepth | tools for manipulating depth concepts for rooted DAGs |
exns2 | Class "namedSparse" adds margin names to sparse matrices |
exptArchive-class | Vocabulary for genomic data integration |
exptSample-class | Vocabulary for genomic data integration |
GDILabel | Structures for working with formal nomenclatures |
GDILabel-class | Vocabulary for genomic data integration |
GDIontology | Structures for working with formal nomenclatures |
GDIontology-class | Vocabulary for genomic data integration |
GDIplatform-class | Vocabulary for genomic data integration |
GDI_NCIThesaurus | Structures for working with formal nomenclatures |
getDefs | Structures for working with formal nomenclatures |
getDefs-method | Structures for working with formal nomenclatures |
getMatrix | matrix utilities for ontoTools. |
getMatrix-method | Class "rootedDAG" |
getTerms | Structures for working with formal nomenclatures |
getTerms-method | Vocabulary for genomic data integration |
go1.15DAG | resources saved for computation of concept probabilities for GO MF |
GOMF1.15 | resources saved for computation of concept probabilities for GO MF |
gomfAmat | sparse matrix representing accessibilities of terms in GO MF graph; |
goMFamat.1.15 | resources saved for computation of concept probabilities for GO MF |
goMFamat.1.4 | resources saved for computation of concept probabilities for GO MF |
goMFgraph.1.15 | resources saved for computation of concept probabilities for GO MF |
goMFgraph.1.4 | resources saved for computation of concept probabilities for GO MF |
goMFgraphDemo | sparse matrix representing accessibilities of terms in GO MF graph; |
grep-method | Vocabulary for genomic data integration |
grList | Class "compoundGraph" list representation of multiple graph::graph |
grList-method | Class "compoundGraph" list representation of multiple graph::graph |
Iyer517 | object-term mapping for human locuslink entries and GO MF |
litObj | litOnto: graph illustrating the ontology concept; litObj: matrix |
litOnto | litOnto: graph illustrating the ontology concept; litObj: matrix |
LL2GOMFcp.1.15 | resources saved for computation of concept probabilities for GO MF |
LL2GOMFcp.1.4 | resources saved for computation of concept probabilities for GO MF |
LL2GOMFooc1.15 | resources saved for computation of concept probabilities for GO MF |
LL2GOMFooMap.1.15 | resources saved for computation of concept probabilities for GO MF |
LL2GOMFooMap.1.4 | resources saved for computation of concept probabilities for GO MF |
LLGOMFcp | resources saved for computation of concept probabilities for GO MF |
makeNamedSparse | Class "namedSparse" adds margin names to sparse matrices |
makeOntology | Class "ontology" wraps a rooted DAG with some ontology metadata |
makeOOC | Class "OOC" object-ontology complex |
makeSparseZero | Class "namedSparse" adds margin names to sparse matrices |
mapNamesInds | Class "namedSparse" adds margin names to sparse matrices |
mat | Class "namedSparse" adds margin names to sparse matrices |
mat-method | Class "namedSparse" adds margin names to sparse matrices |
maxval | Class "namedSparse" adds margin names to sparse matrices |
maxval-method | Class "namedSparse" adds margin names to sparse matrices |
mkNS | Class "namedSparse" adds margin names to sparse matrices |
name | Class "ontology" wraps a rooted DAG with some ontology metadata |
name-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
namedSparse-class | Class "namedSparse" adds margin names to sparse matrices |
ncol-method | Class "namedSparse" adds margin names to sparse matrices |
newadj | matrix utilities for ontoTools. |
nomenclature-class | Vocabulary for genomic data integration |
nrow-method | Class "namedSparse" adds margin names to sparse matrices |
nsparse | Class "namedSparse" adds margin names to sparse matrices |
ontoDepth | tools for manipulating depth concepts for rooted DAGs |
ontology | Class "ontology" wraps a rooted DAG with some ontology metadata |
ontology-class | Class "ontology" wraps a rooted DAG with some ontology metadata |
ontology-method | Class "OOC" object-ontology complex |
OOC-class | Class "OOC" object-ontology complex |
OOmap | Class "OOC" object-ontology complex |
OOmap-method | Class "OOC" object-ontology complex |
ooMapLL2GOMFdemo | object-term mapping for human locuslink entries and GO MF |
otkvEnv2namedSparse | obtain sparse matrix representation of key-value structures |
otkvList2namedSparse | obtain sparse matrix representation of key-value structures |
OVersion | Class "ontology" wraps a rooted DAG with some ontology metadata |
OVersion-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
parents | Structures for working with formal nomenclatures |
parents-method | Class "taggedHierNomenclature" ~~~ |
pms | Compute semantic similarity measure for terms in an object-ontology |
provStruct | Structures for working with formal nomenclatures |
provStruct-class | Vocabulary for genomic data integration |
rDAG | Class "ontology" wraps a rooted DAG with some ontology metadata |
rDAG-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
revArcs | matrix utilities for ontoTools. |
root | Class "rootedDAG" |
root-method | Class "rootedDAG" |
rootedDAG-class | Class "rootedDAG" |
rowinds | Class "namedSparse" adds margin names to sparse matrices |
rowinds-method | Class "namedSparse" adds margin names to sparse matrices |
rowSums | Class "namedSparse" adds margin names to sparse matrices |
rowSums-method | Class "namedSparse" adds margin names to sparse matrices |
rowSumsSp | Class "namedSparse" adds margin names to sparse matrices |
semsim | Compute semantic similarity measure for terms in an object-ontology |
SGDIvocab | Vocabulary for genomic data integration |
show-method | Structures for working with formal nomenclatures |
show-method | Class "OOC" object-ontology complex |
show-method | Vocabulary for genomic data integration |
show-method | Class "namedSparse" adds margin names to sparse matrices |
show-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
show-method | Class "taggedHierNomenclature" ~~~ |
STMA | Vocabulary from statistics theory and methods abstracts |
subsumers | Compute semantic similarity measure for terms in an object-ontology |
sumSp | Class "namedSparse" adds margin names to sparse matrices |
sumSpSLOW | Class "namedSparse" adds margin names to sparse matrices |
symMapping-class | Vocabulary for genomic data integration |
t-method | Class "namedSparse" adds margin names to sparse matrices |
taggedHierNomenclature | Class "taggedHierNomenclature" ~~~ |
taggedHierNomenclature-class | Class "taggedHierNomenclature" ~~~ |
thesList | Structures for working with formal nomenclatures |
toDot | Methods for Function toDot in Package 'ontoTools' - should be replaced |
toDot-method | Class "compoundGraph" list representation of multiple graph::graph |
toDot-method | Methods for Function toDot in Package 'ontoTools' - should be replaced |
typedSymMapping-class | Vocabulary for genomic data integration |
usageCount | Compute semantic similarity measure for terms in an object-ontology |
[-method | Class "namedSparse" adds margin names to sparse matrices |