A B C D E F G H I K L M N O P Q R S T U V W misc
CellMix-package | Gene Expression Deconvolution |
Abbas | Basis Matrix for Whole Blood Expression Deconvolution |
Abbas-markers | Optimised Set of Marker Genes for Immune Cells |
addNames | Generating Names |
annotation | Accessing Data in Marker Lists |
annotation-method | Accessing Data in Marker Lists |
annotation-methods | Accessing Data in Marker Lists |
annotation<- | Accessing Data in Marker Lists |
annotation<--method | Accessing Data in Marker Lists |
annotation<--methods | Accessing Data in Marker Lists |
anyRequired | Checking Input and Output Data for GED Algorithms |
applyBy | Group Apply |
applyBy.ExpressionSet | Group Apply |
applyBy.matrix | Group Apply |
asCBC | Blood Sample Deconvolution |
asCBC-method | Blood Sample Deconvolution |
asCBC-methods | Blood Sample Deconvolution |
asGeneIdentifierType | Utility function for Biological Identifiers |
attachMarkers | Class for Marker Gene Lists |
barplot.MarkerList | Plotting MarkerList Objects |
basis-method | Accessing Data from CellMix Dataset |
basisfit | Accessing Fit Data in Deconvolution Results |
basismarkermap | Heatmaps Highlighting Markers |
beeswarm.MarkerList | Plotting Markers |
bioc2gpl | Mapping Bioconductor Annotation packages to GEO GPL Identifiers |
biocann_map | Retrieving ID Conversion Maps |
biocann_mapname | Annotation Tools |
biocann_object | Retrieving Bioconductor Annotation Maps |
biocann_pkgname | Annotation Tools |
biocann_pkgobject | Annotation Tools |
boxplotBy | Split Boxplot by Group |
boxplotBy.default | Split Boxplot by Group |
boxplotBy.NMF | Split Boxplot by Group |
cbind.ExpressionSet | Combining Expression Matrices |
cellMarkers | Loading Marker Lists from Registry |
cellMarkersInfo | Loading Marker Lists from Registry |
CellMix | Gene Expression Deconvolution |
cellmix.getOption | Package Specific Options for CellMix |
cellmix.options | Package Specific Options for CellMix |
cellmix.printOptions | Package Specific Options for CellMix |
cellmix.resetOptions | Package Specific Options for CellMix |
checkConstraints | Checking Linear Constraints |
checkS4 | Validity Functions of Registry Fields |
coef-method | Accessing Data from CellMix Dataset |
coeffit | Accessing Fit Data in Deconvolution Results |
colApplyBy | Group Apply |
colMaxsBy | Group Apply |
colMeansBy | Group Apply |
colMediansBy | Group Apply |
colMinsBy | Group Apply |
colSumsBy | Group Apply |
combine-method | Combine markers from multiple cell types of a MarkerList object, based on groups defined by a given factor. |
Compare-method | Operations on MarkerList Objects |
connectivity | Accessing Data in Marker Lists |
connectivity-method | Accessing Data in Marker Lists |
connectivity-methods | Accessing Data in Marker Lists |
convertIDs | Converting Gene or Probeset IDs |
convertIDs-method | Converting Gene or Probeset IDs |
convertIDs-methods | Converting Gene or Probeset IDs |
cs-lsfit-ged | Cell-Specific Expression by Standard Least-Squares |
cs-qprog-ged | Partial Gene Expression Deconvolution by Quadratic Programming |
csplot | Plots Cell-Specific FDR Estimates |
csplot.character | Plots Cell-Specific FDR Estimates |
csplot.csSAM | Partial Gene Expression Deconvolution with csSAM |
csplot.NMFfit | Plots Cell-Specific FDR Estimates |
csplot.NMFfitX | Plots Cell-Specific FDR Estimates |
csSAM-ged | Partial Gene Expression Deconvolution with csSAM |
csTopTable | Compute Cell-Specific Statistics |
csTopTable.array | Compute Cell-Specific Statistics |
csTopTable.character | Compute Cell-Specific Statistics |
csTopTable.csSAM | Partial Gene Expression Deconvolution with csSAM |
csTopTable.DSection | Partial Gene Expression Deconvolution with DSection |
csTopTable.matrix | Compute Cell-Specific Statistics |
csTopTable.NMFfit | Compute Cell-Specific Statistics |
csTopTable.NMFfitX | Compute Cell-Specific Statistics |
DataSource | Gene Expression Data Sources |
deconf-ged | Complete Gene Expression Deconvolution: Method deconf |
details | Accessing Data in Marker Lists |
details-method | Accessing Data in Marker Lists |
details-methods | Accessing Data in Marker Lists |
dim-method | Dimensions in ExpressionMix Objects |
dimnames-method | Dimensions in ExpressionMix Objects |
dimnames<--method | Dimensions in ExpressionMix Objects |
dims-method | Accessing Data from CellMix Dataset |
drop-method | Utility Functions for MarkerList Objects |
dropvalues | Utility Functions for MarkerList Objects |
DSA-ged | Complete Deconvolution using Digital Sorting Algorithm (DSA) |
DSAproportions | Digital Sorting Algorithm: Proportion Estimation Method |
DSection | DSection Gene Expression Deconvolution Method |
DSection-ged | Partial Gene Expression Deconvolution with DSection |
enforceMarkers | Enforcing Marker Block Patterns |
enforceMarkers-method | Enforcing Marker Block Patterns |
enforceMarkers-methods | Enforcing Marker Block Patterns |
eset | Extracting Expression Data |
eset-method | Extracting Expression Data |
eset-methods | Extracting Expression Data |
exp-method | Numeric Computations on ExpressionSet objects |
expb | Numeric Computations on ExpressionSet objects |
expb-method | Numeric Computations on ExpressionSet objects |
expb-methods | Numeric Computations on ExpressionSet objects |
ExpressionMix | Factory Method for ExpressionMix Objects |
ExpressionMix-class | Class for Gene Expression Deconvolution Benchmark Datasets |
ExpressionMix-method | Factory Method for ExpressionMix Objects |
ExpressionMix-methods | Factory Method for ExpressionMix Objects |
ExpressionMix-subset | Subsetting ExpressionMix Objects |
exprs | Extracting Feature Names |
exprs-method | Extracting Feature Names |
exprs-method | Accessing Data from CellMix Dataset |
exprs-methods | Extracting Feature Names |
extractMarkers | Extract Markers from Pure Samples. |
extractMarkers-method | Extract Markers from Pure Samples. |
extractMarkers-methods | Extract Markers from Pure Samples. |
featureNames | Extracting Feature Names |
featureNames-method | Extracting Feature Names |
featureNames-methods | Extracting Feature Names |
featureNames<- | Extracting Feature Names |
featureNames<--method | Dimensions in ExpressionMix Objects |
featureNames<--methods | Extracting Feature Names |
fetchData | Fetching Data from Data Sources |
flatten | Flattening Marker Lists |
flatten-method | Flattening Marker Lists |
flatten-methods | Flattening Marker Lists |
gCBC | Blood Sample Deconvolution |
ged | Main Interface for Gene Expression Deconvolution Methods |
ged-method | Main Interface for Gene Expression Deconvolution Methods |
ged-methods | Main Interface for Gene Expression Deconvolution Methods |
gedAlgorithm | Managing Gene Expression Deconvolution Algorithms |
gedAlgorithm.csSAM | Partial Gene Expression Deconvolution with csSAM |
gedAlgorithm.cs_lsfit | Cell-Specific Expression by Standard Least-Squares |
gedAlgorithm.cs_qprog | Partial Gene Expression Deconvolution by Quadratic Programming |
gedAlgorithm.deconf | Complete Gene Expression Deconvolution: Method deconf |
gedAlgorithm.DSA | Complete Deconvolution using Digital Sorting Algorithm (DSA) |
gedAlgorithm.DSection | Partial Gene Expression Deconvolution with DSection |
gedAlgorithm.lsfit | Partial Gene Expression Deconvolution by Standard Least-Squares |
gedAlgorithm.meanProfile | Partial Gene Expression Deconvolution: Marker Mean Expression Profile |
gedAlgorithm.qprog | Partial Gene Expression Deconvolution by Quadratic Programming |
gedAlgorithm.ssFrobenius | Complete Gene Expression Deconvolution by Semi-Supervised NMF |
gedAlgorithm.ssKL | Complete Gene Expression Deconvolution by Semi-Supervised NMF |
gedAlgorithmInfo | Managing Gene Expression Deconvolution Algorithms |
gedBlood | Blood Sample Deconvolution |
gedCheck | Checking a Deconvolution Method |
gedData | Loading Gene Expression Deconvolution Data |
GEDdata-access | Accessing Data from CellMix Dataset |
gedDataInfo | Loading Gene Expression Deconvolution Data |
GEDdownload | Downloading Gene Expression Deconvolution Datasets |
gedInput | Checking Input and Output Data for GED Algorithms |
gedIO | Checking Input and Output Data for GED Algorithms |
gedOutput | Checking Input and Output Data for GED Algorithms |
gedProportions | Estimating Cell Proportions from Known Signatures |
GEDStrategy | Factory Methods for GEDStrategy Objects |
GEDStrategy-class | Class for GED Algorithms |
GEDStrategy-method | Factory Methods for GEDStrategy Objects |
GEDStrategy-methods | Factory Methods for GEDStrategy Objects |
geneIds | Accessing Data in Marker Lists |
geneIds-method | Accessing Data in Marker Lists |
geneIds-methods | Accessing Data in Marker Lists |
geneIds<- | Accessing Data in Marker Lists |
geneIds<--method | Accessing Data in Marker Lists |
geneIds<--methods | Accessing Data in Marker Lists |
geneIdType | Accessing Data in Marker Lists |
geneIdType-method | Accessing Data in Marker Lists |
geneIdType-methods | Accessing Data in Marker Lists |
geneIdType<- | Accessing Data in Marker Lists |
geneIdType<--method | Accessing Data in Marker Lists |
geneIdType<--methods | Accessing Data in Marker Lists |
geneValues | Accessing Data in Marker Lists |
geneValues-method | Accessing Data in Marker Lists |
geneValues-methods | Accessing Data in Marker Lists |
geneValues<- | Accessing Data in Marker Lists |
geneValues<--methods | Accessing Data in Marker Lists |
getAnnotation | Extracting Annotation from Objects |
getGSE | Downloading GSE Datasets from GEO |
getMarkers | Class for Marker Gene Lists |
gMarkerList | Generating Marker Lists |
gmarkers | Generating Marker Lists |
GPL2bioc | Map Between Bioconductor Annotation Packages and GEO GPL Identifiers |
gpl2bioc | Mapping Bioconductor Annotation packages to GEO GPL Identifiers |
Grigoryev-markers | Grigoryev - Cytometry Antigen Markers |
GSE11058_pdata | Cell Line Proportions for Dataset GSE11058 |
GSE20300_pdata | Complete Blood Count for Dataset GSE20300 |
GSE3649_fdata | Feature Annotation Data for Dataset GSE3649 |
GSE3649_pdata | Phenotypic Annotation Data for Dataset GSE3649 |
HaemAtlas | HaemAtlas Dataset - Immune Cells |
HaemAtlas-markers | HaemAtlas Marker List for Immune Cells - Watkins et al. (2009) |
has.markers | Class for Marker Gene Lists |
hasAnnotation | Extracting Annotation from Objects |
hasDuplicated | Utility Functions for MarkerList Objects |
hasValues | Accessing Data in Marker Lists |
hist.MarkerList | Plotting Markers |
idFilter | Gene Identifier Filtering Strategies |
idFilterAffy | Gene Identifier Filtering Strategies |
idFilterAll | Gene Identifier Filtering Strategies |
idFilterAuto | Gene Identifier Filtering Strategies |
idFilterFirstN | Gene Identifier Filtering Strategies |
idFilterInjective | Gene Identifier Filtering Strategies |
idFilterMAuto | Gene Identifier Filtering Strategies |
idFilterOneToMany | Gene Identifier Filtering Strategies |
idFilterOneToOne | Gene Identifier Filtering Strategies |
idtype | Identifying Gene or Probe ID Type |
idtype-method | Identifying Gene or Probe ID Type |
idtype-methods | Identifying Gene or Probe ID Type |
incidence | Accessing Data in Marker Lists |
incidence-method | Accessing Data in Marker Lists |
incidence-methods | Accessing Data in Marker Lists |
initialize-method | Initialize method for ExpressionMix object |
intersect | Enhanced Subsetting for Matrix-like Data |
intersect-method | Enhanced Subsetting for Matrix-like Data |
IRIS | Immune Response In-Silico (IRIS) Data |
IRIS-markers | Marker Genes for Immune Cells (IRIS) |
is.anndb | Annotation Tools |
is.annpkg | Annotation Tools |
is.idtype | Utility function for Biological Identifiers |
is.probeid | Utility function for Biological Identifiers |
is.probetype | Utility function for Biological Identifiers |
isDataSource | Gene Expression Data Sources |
isMarkerList | Class for Marker Gene Lists |
isRequired | Checking Input and Output Data for GED Algorithms |
is_logscale | Detect Log-transformed Data |
kappa.MarkerList | Condition Number of a Marker List |
log-method | Numeric Computations on ExpressionSet objects |
log_transform | Detect Log-transformed Data |
lpure | Acessing Pure or Mixed Sample Data |
lsfit-ged | Partial Gene Expression Deconvolution by Standard Least-Squares |
mapIdentifiers-method | Converting Gene or Probeset IDs |
mapIDs | Mapping Gene Identifiers |
MarkerList | Factory Method for Marker Lists |
MarkerList-class | Class for Marker Gene Lists |
MarkerList-method | Factory Method for Marker Lists |
MarkerList-methods | Factory Method for Marker Lists |
markermap | Heatmaps Highlighting Markers |
markermap-method | Heatmaps Highlighting Markers |
markermap-methods | Heatmaps Highlighting Markers |
markerScoreAbbas | Marker Scoring Method: Abbas et al. (2009) |
markerScoreHSD | Marker Scoring Method: Tukey Honest Significant Difference |
markerScoreMaxcol | Marker scoring method: Max Expression |
markerScoreMethod | Extract Markers from Pure Samples. |
markerScoreScorem | Marker scoring method: SCOREM |
MarkerSetCollection | Factory Methods for Marker Gene Set Collections |
MarkerSetCollection-class | Classes for Marker Gene Set Collections |
MarkerSetCollection-methods | Factory Methods for Marker Gene Set Collections |
markersGrigoryev | Cytometry Antigen Expression from Grigoryev et al. (2010) |
marknames | Accessing Data in Marker Lists |
marknames-method | Accessing Data in Marker Lists |
marknames-methods | Accessing Data in Marker Lists |
match.cell | Assigning Estimated Signature to Real Cell-Types |
match.nmf | Assigning Estimated Signature to Real Cell-Types |
matchIndex | Creating Mapping from Marker Lists |
matchIndex-method | Creating Mapping from Marker Lists |
matchIndex-methods | Creating Mapping from Marker Lists |
match_first | Returns the index of the first match in a reference table |
meanProfile-ged | Partial Gene Expression Deconvolution: Marker Mean Expression Profile |
mergeList | Merge two lists |
mixData | Extracting Mixture Data |
mixData-method | Extracting Mixture Data |
mixData-methods | Extracting Mixture Data |
mixData<- | Extracting Mixture Data |
mixData<--method | Extracting Mixture Data |
mixData<--methods | Extracting Mixture Data |
mixedSamples | Acessing Pure or Mixed Sample Data |
mlsei | Multivariate Least Squares with Equalities and Inequalities |
mltype | Utility Functions for MarkerList Objects |
MySQLtoSQLite | Load a MySQL Dump for Using with SQLite |
nbasis-method | Accessing Data from CellMix Dataset |
nmark | Utility Functions for MarkerList Objects |
nmark-method | Utility Functions for MarkerList Objects |
nmark-methods | Utility Functions for MarkerList Objects |
nmf | Accessing Data in Marker Lists |
nmf-method | Accessing Data in Marker Lists |
nmf-methods | Accessing Data in Marker Lists |
npure | Acessing Pure or Mixed Sample Data |
nuIDdecode | Convert nuID to Nucleotide Sequence |
onlyRequired | Checking Input and Output Data for GED Algorithms |
Palmer | Palmer Dataset |
profplot.MarkerList | Plotting Markers |
propplot | Cell Type Proportion Plot |
pureSamples | Acessing Pure or Mixed Sample Data |
qprog-ged | Partial Gene Expression Deconvolution by Quadratic Programming |
quantile.ExpressionSet | Numeric Computations on ExpressionSet objects |
range-method | Numeric Computations on ExpressionSet objects |
refCBC | Blood Sample Deconvolution |
regcheck | Validity Functions of Registry Fields |
removeGEDMethod | Register CellMix Deconvolution Methods |
removeMarkerList | Register CellMix MarkerLists |
reorder-method | Reordering Marker Lists |
reverse | Utility Functions for MarkerList Objects |
reverse-method | Utility Functions for MarkerList Objects |
reverse-methods | Utility Functions for MarkerList Objects |
revmap-method | Annotation Tools |
rMarkerList | Generating Marker Lists |
rmarkers | Generating Marker Lists |
rmDuplicated | Utility Functions for MarkerList Objects |
rmix | Generating Random Global Mixed Gene Expression Data |
rowApplyBy | Group Apply |
rowMaxsBy | Group Apply |
rowMeansBy | Group Apply |
rowMediansBy | Group Apply |
rowMinsBy | Group Apply |
rowSumsBy | Group Apply |
rproportions | Generating Random Cell Type Proportions |
rpure | Generating Random Pure Cell Type Sample |
sampleNames | Extracting Feature Names |
sampleNames-method | Extracting Feature Names |
sampleNames-methods | Extracting Feature Names |
sampleNames<- | Extracting Feature Names |
sampleNames<--method | Dimensions in ExpressionMix Objects |
sampleNames<--methods | Extracting Feature Names |
sapply-method | Aplying Functions Along MarkerList Objects |
scoreMarkers | Extract Markers from Pure Samples. |
screeplot.MarkerList | Plotting Markers |
selectGEDMethod | Automatic Selection of Gene Expression Deconvolution Algorithms |
selectMarkers | Select Markers Based on Scores |
selectMarkers.MarkerList | Select Markers Based on Scores |
selectMarkers.markerScore | Select Markers Based on Scores |
selectMarkers.markerScore_HSD | Marker Scoring Method: Tukey Honest Significant Difference |
selectMarkers.markerScore_scorem | Marker scoring method: SCOREM |
setAnnotation | Extracting Annotation from Objects |
setGEDMethod | Register CellMix Deconvolution Methods |
setMarkerList | Register CellMix MarkerLists |
show-method | Factory Method for ExpressionMix Objects |
show-method | Class for GED Algorithms |
show-method | Accessing Data in Marker Lists |
showData | Show Data Available in an Object |
showData-method | Show Data Available in an Object |
showData-methods | Show Data Available in an Object |
SLE | Gene Expression from Systemic Lupus Erythematosus Patients |
sort.MarkerList | Reordering Marker Lists |
ssFrobenius-ged | Complete Gene Expression Deconvolution by Semi-Supervised NMF |
ssKL-ged | Complete Gene Expression Deconvolution by Semi-Supervised NMF |
stack.MarkerList | Converting Marker Lists into data.frames |
stripchart.MarkerList | Plotting Markers |
subset-method | Subsetting Marker Lists |
subsetML | Subsetting Data with MarkerList Objects |
summary-method | Class for Marker Gene Lists |
TDDB_HS | Human Tissue Specific Genes from the TissueDistributionDB Database |
TDDB_RN | Rat Tissue Specific Genes from the TissueDistributionDB Database |
TIGER | TiGER Database |
TIGER-markers | TiGER - Human Tissue Specific Genes |
TissueDistributionDB_HS | Human Tissue Specific Genes from TissueDistributionDB |
TissueDistributionDB_HS-markers | Human Tissue Specific Genes from the TissueDistributionDB Database |
TissueDistributionDB_RN | Rat Tissue Specific Genes from TissueDistributionDB |
TissueDistributionDB_RN-markers | Rat Tissue Specific Genes from the TissueDistributionDB Database |
unstack.stackedMarkerList | Converting Marker Lists into data.frames |
userData | User Data Directory |
VeryGene | VeryGene Dataset |
VeryGene-markers | VeryGene - Marker List for Human Tissues |
wpure | Acessing Pure or Mixed Sample Data |
.atrack-method | Heatmap Annotation Track for MarkerList Objects |
.csSAM | Cell-specific Differential Expression with csSAM |
.DollarNames-method | Auto-completion for 'ExpressionMix' objects |
.DSAproportions | Digital Sorting Algorithm: Proportion Estimation Method |
.mAbbas | Optimised Set of Marker Genes for Immune Cells |
.mHaemAtlas | HaemAtlas Marker List for Immune Cells - Watkins et al. (2009) |
.mIRIS | Marker Genes for Immune Cells (IRIS) |
.mTDDB_HS | Human Tissue Specific Genes from the TissueDistributionDB Database |
.mTDDB_RN | Rat Tissue Specific Genes from the TissueDistributionDB Database |
.mTIGER | TiGER - Human Tissue Specific Genes |
[-method | Subsetting ExpressionMix Objects |
[-method | Subsetting Marker Lists |