C D E F G I K L M N P R S T U W Z misc
gCMAP-package | Tools for Connectivity Map-like analyses |
camera_score | Methods for Function 'camera_score' in Package 'gCMAP' |
camera_score-method | Methods for Function 'camera_score' in Package 'gCMAP' |
camera_score-methods | Methods for Function 'camera_score' in Package 'gCMAP' |
center_eSet | A function to to center columns of eSet channels on either their kernel density peak, their mean or their median. |
CMAPCollection | Class '"CMAPCollection"' |
CMAPCollection-class | Class '"CMAPCollection"' |
CMAPCollection-method | Class '"CMAPCollection"' |
CMAPResults | Class '"CMAPResults"' |
CMAPResults-class | Class '"CMAPResults"' |
cmapTable | Class '"CMAPResults"' |
cmapTable-method | Class '"CMAPResults"' |
connectivity_score | Broad CMAP gene set enrichment metrics |
connectivity_score-method | Broad CMAP gene set enrichment metrics |
docs | Class '"CMAPResults"' |
docs-method | Class '"CMAPResults"' |
docs<- | Class '"CMAPResults"' |
docs<--method | Class '"CMAPResults"' |
downIds | Class '"SignedGeneSet"' |
downIds-method | Class '"SignedGeneSet"' |
effect | Class '"CMAPResults"' |
effect-method | Class '"CMAPResults"' |
effect<- | Class '"CMAPResults"' |
effect<--method | Class '"CMAPResults"' |
errors | Class '"CMAPResults"' |
errors-method | Class '"CMAPResults"' |
errors<- | Class '"CMAPResults"' |
errors<--method | Class '"CMAPResults"' |
eSetOnDisk | A function to store the assayData of an eSet object as BigMatrix files on disk. |
featureScores | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
featureScores-method | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
featureScores-methods | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
fisher_score | Hypergeometric probability of gene set enrichment |
fisher_score-method | Hypergeometric probability of gene set enrichment |
fisher_score-methods | Hypergeometric probability of gene set enrichment |
gCMAP | Tools for Connectivity Map-like analyses |
gCMAPData | Example 'NChannelSet' |
GeneColorSet-method | Methods for 'GeneSet' and 'GeneColorSet' |
geneIds-method | Class '"CMAPCollection"' |
geneIndex | Methods for Function 'geneIndex' in Package 'gCMAP' |
geneIndex-method | Methods for Function 'geneIndex' in Package 'gCMAP' |
geneIndex-methods | Methods for Function 'geneIndex' in Package 'gCMAP' |
generate_gCMAP_NChannelSet | Generate a perturbation profile library from expression sets of control/treatment pairs |
geneScores | Class '"CMAPResults"' |
geneScores-method | Class '"CMAPResults"' |
GeneSet | Methods for 'GeneSet' and 'GeneColorSet' |
GeneSet-method | Methods for 'GeneSet' and 'GeneColorSet' |
geneSign | Class '"SignedGeneSet"' |
geneSign-method | Class '"SignedGeneSet"' |
geneSign<- | Class '"SignedGeneSet"' |
geneSign<--method | Class '"SignedGeneSet"' |
gsealm_jg_score | Parametric test for testing normally distributed scores for gene set enrichment |
gsealm_jg_score-method | Parametric test for testing normally distributed scores for gene set enrichment |
gsealm_jg_score-methods | Parametric test for testing normally distributed scores for gene set enrichment |
gsealm_score | Methods for Function 'gsealm_score' in Package 'gCMAP' |
gsealm_score-method | Methods for Function 'gsealm_score' in Package 'gCMAP' |
gsealm_score-methods | Methods for Function 'gsealm_score' in Package 'gCMAP' |
incidence-method | Class '"CMAPCollection"' |
incidence-method | Class '"SignedGeneSet"' |
induceCMAPCollection | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
induceCMAPCollection-method | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
induceCMAPCollection-methods | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
initialize-method | Class '"CMAPCollection"' |
initialize-method | Class '"CMAPResults"' |
initialize-method | Class '"SignedGeneSet"' |
ks | Broad CMAP gene set enrichment metrics |
labels | Class '"CMAPResults"' |
labels-method | Class '"CMAPResults"' |
labels<- | Class '"CMAPResults"' |
labels<--method | Class '"CMAPResults"' |
mapIdentifiers-method | Class '"SignedGeneSet"' |
mapNmerge | A function to map eSet featureNames and calculate summaries for many-to-one mapping features |
members | Class '"CMAPCollection"' |
members-method | Class '"CMAPCollection"' |
memorize | Create a new NChannelSet instance by selecting specific channels and load BigMatrix assayData into memory, if present |
mergeCollections | Class '"CMAPCollection"' |
mergeCollections-method | Class '"CMAPCollection"' |
minSetSize | GeneSetCollection length filtering |
minSetSize-method | GeneSetCollection length filtering |
mroast_score | Methods for Function 'mroast_score' in Package 'gCMAP' |
mroast_score-method | Methods for Function 'mroast_score' in Package 'gCMAP' |
mroast_score-methods | Methods for Function 'mroast_score' in Package 'gCMAP' |
nFound | Class '"CMAPResults"' |
nFound-method | Class '"CMAPResults"' |
nFound<- | Class '"CMAPResults"' |
nFound<--method | Class '"CMAPResults"' |
nSet | Class '"CMAPResults"' |
nSet-method | Class '"CMAPResults"' |
nSet<- | Class '"CMAPResults"' |
nSet<--method | Class '"CMAPResults"' |
padj | Class '"CMAPResults"' |
padj-method | Class '"CMAPResults"' |
padj<- | Class '"CMAPResults"' |
padj<--method | Class '"CMAPResults"' |
pairwise_compare | Generate statistics associated with pairwise differential expression |
pairwise_compare_limma | Generate statistics associated with pairwise differential expression |
pairwise_DESeq | Generate statistics associated with pairwise differential expression from RNAseq count data |
plot-method | Class '"CMAPResults"' |
pval | Class '"CMAPResults"' |
pval-method | Class '"CMAPResults"' |
pval<- | Class '"CMAPResults"' |
pval<--method | Class '"CMAPResults"' |
romer_score | Methods for Function 'romer_score' in Package 'gCMAP' |
romer_score-method | Methods for Function 'romer_score' in Package 'gCMAP' |
romer_score-methods | Methods for Function 'romer_score' in Package 'gCMAP' |
S | Broad CMAP gene set enrichment metrics |
s | Broad CMAP gene set enrichment metrics |
set | Class '"CMAPResults"' |
set-method | Class '"CMAPResults"' |
set<- | Class '"CMAPResults"' |
set<--method | Class '"CMAPResults"' |
show-method | Class '"CMAPResults"' |
show-method | Class '"SignedGeneSet"' |
signed | Class '"CMAPCollection"' |
signed-method | Class '"CMAPCollection"' |
signed<- | Class '"CMAPCollection"' |
signed<--method | Class '"CMAPCollection"' |
SignedGeneSet | Construtor for SignedGeneSet |
SignedGeneSet-class | Class '"SignedGeneSet"' |
SignedGeneSet-method | Construtor for SignedGeneSet |
signedRankSumTest | An implementation of the Wilcox rank sum test / Mann-Whitney test that takes into account the direction / sign of gene set members and possibly the correlation between cases |
trend | Class '"CMAPResults"' |
trend-method | Class '"CMAPResults"' |
trend<- | Class '"CMAPResults"' |
trend<--method | Class '"CMAPResults"' |
upIds | Class '"SignedGeneSet"' |
upIds-method | Class '"SignedGeneSet"' |
wilcox_score | Methods for Function 'wilcox_score' in Package 'gCMAP' |
wilcox_score-method | Methods for Function 'wilcox_score' in Package 'gCMAP' |
wilcox_score-methods | Methods for Function 'wilcox_score' in Package 'gCMAP' |
zScores | Function to calculate z-scores from p-values |
zscores | Class '"CMAPResults"' |
zscores-method | Class '"CMAPResults"' |
.DESeq_nbinom | Function to perform a DESeq analysis to detect differential expression between perturbation and control groups. |