addPhenoDataDS | Add Phenotype data to ExpressionSet |
alleleFrequencyDS | Allelic frequency |
BAM2VCF | Variant discovery on a BAM file |
cellCountsDS | Estimate cell counts from methylation data |
computeN | Compute N |
createRSEDS | create a RangedSummarizedExperiment from a RNAseq count table... |
DESeq2DS | Differential expression analysis on the server-side |
dlaplace | Random laplace distribution generator |
dot-fittedValues_exponential | Fit values for binomial model |
dot-fittedValues_linear | Fit values for linear model |
dot-one_hot_encoding | Create dummy variables |
dot-retrievePGS | Internal function: Get PGS catalog table of polygenic risks |
edgeRDS | Differential expression analysis on the server-side |
EGAhtsgetResourceClient | EGA htsget resource client |
EGAhtsgetResourceResolver | EGA htsget resource resolver |
exactHWEDS | Hardy-Weinberg Equilibrium testing |
extractPhenoFromGDSDS | Extract phenotype table from GenotypeData object |
fastAlleleFrequencyDS | Allelic frequency |
fastGWAS_ColSums | Get colsums needed for fast GWAS |
fastGWAS_getFitted.values | Obtain fitted values given coefficients, family and values... |
fastGWAS_getResiduals | Obtain residual values given fitted values, family and... |
fastGWAS_PHENO_removeNAindiv | Remove individuals from the phenotype that have NAs on any of... |
fastGWAS_S | Extract Geno iterator and Pheno information from GenotypeData... |
fastGWAS_S_means | Get mean of the genotype by individual |
featureDataDS | Retrieve information on features recorded in eSet-derived... |
featureNamesDS | Retrieve feature names from eSets. |
fvarLabelsDS | Retrieve names of annotation from eSets. |
GA4GHResourceClient | GA4GH htsget server resource client |
GA4GHResourceResolver | GA4GH htsget server resource resolver |
GDSFileResourceClient | GDS file resource client |
GDSFileResourceResolver | GDS file resource resolver |
gdsSubset2 | Write a subset of data in a GDS file to a new GDS file |
genoDimensionsDS | Get main dimensions of Genotype data |
geno_pca_pooled_addPC2GenoDS | Add PCA results to the phenotype slot |
geno_pca_pooled_addPCDS | Add PCA results to geno |
GenotypeDataDS | Class GenotypeData. |
getChromosomeNamesDS | Get names of chromosomes |
getSNPSbyGenDS | Subset GDS with gene(s) |
getVariable | Get slot of GDS object |
GWASDS | Genome-wide association analysis (GWAS) on the server-side |
Laplace_noise_generator | Random laplace generator |
limmaDS | Differential expression analysis using limma on the... |
limmaDS2 | Differential expression analysis using limma on the... |
make_valid_namesDS | Rename column names and character variables |
methylation_array_convertDS | Convert a Methylation ExpressionSet from EPIC to 450k Array |
nFeaturesDS | Retrieve number of features from eSets and... |
nSamplesDS | Retrieve number of samples from eSets and... |
Opal2FileResourceGetter | Opal file resource getter |
PCADS | Principal Component Analysis (PCA) on SNP genotype data |
PCASNPSDS | Principal Component Analysis (PCA) on SNP genotype data |
pDataDS | Retrieve information on experimental phenotypes recorded in... |
plinkDS | Genome-wide association analysis (GWAS) using PLINK |
plotPCADS | Grouping to plot PCA |
plotPCASNPSDS | Grouping to plot PCA |
PRSDS | Get Ploygenic Risk Score |
PRSDS_aux | Auxiliary function to merge the PRS results to a table by ID |
removeOutliersDS | Filter potential CpG outliers |
rlaplace | Random laplace generator |
RNAseqPreprocDS | Filter Genes By Expression Level |
selFeatureDS | Subset the information of a given feature in a eSet object. |
selSNPDS | Subset the information of a given SNP in a GDS object. |
snptestDS | Interface to run SNPtest commands on a ssh connection (with... |
subsetExpressionSet2DS | Subset ExpressionSet |
subsetExpressionSetDS | Subset ExpressionSet |
subsetGenoDS | Subset genotype |
svdPartial | Partial singular value decomposition |
varLabelsDS | Retrieve feature names from eSets. |
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