Biocview "StatisticalMethod"

Adjust for positional and batch effects using ComBat
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for qualitative biclustering in support of gene co-expression analyses
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
Asymptotic tests and model fitting for extreme phenotype sampling
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Calculates Mulcom test
Calculates Mulcom test
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
Compensates for the bias introduced by median normalization in phosphoproteomics
Compensates for the bias introduced by median normalization in phosphoproteomics
Concomitant identification of distinctness and similarity in gene expression analysis.
Controlling bias and inflation in association studies using the empirical null distribution
Controlling bias and inflation in association studies using the empirical null distribution
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
DeMAND
DeMAND
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detection of DE genes in time series data using impulse models
Detection of DE genes in time series data using impulse models
Detection of DE genes in time series data using impulse models
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayesian approach to mutational signature discovery
Empirical Bayesian approach to mutational signature discovery
Empirical Bayesian approach to mutational signature discovery
FABIA: Factor Analysis for Bicluster Acquisition
FABIA: Factor Analysis for Bicluster Acquisition
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Functional similarities
Functional similarities
Functional similarities
geneChip Analysis Package
geneChip Analysis Package
Gene expression changes in three biological conditions
Gene expression changes in three biological conditions
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Gene Set Analysis in R
Gene Set Analysis in R
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis Extended to Contingency Cubes
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Genometric Correlation package
GISPA: Method for Gene Integrated Set Profile Analysis
GISPA: Method for Gene Integrated Set Profile Analysis
GISPA: Method for Gene Integrated Set Profile Analysis
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
HLA Genotype Imputation with Attribute Bagging
HLA Genotype Imputation with Attribute Bagging
HLA Genotype Imputation with Attribute Bagging
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification of cancer cell lines based on their weighted mutational or variational fingerprint
Identification of cancer cell lines based on their weighted mutational or variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Inferring functionally related proteins using protein interaction networks
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
JODA algorithm for quantifying gene deregulation using knowledge
JODA algorithm for quantifying gene deregulation using knowledge
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
Judging Quality of Clustering Methods using Mutual Information
LEA: an R package for Landscape and Ecological Association Studies
LEA: an R package for Landscape and Ecological Association Studies
Longitudinal system suitability monitoring and quality control for proteomic experiments
Lots Of Lasso
Lots Of Lasso
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Measurement Error model estimate for correlation coefficient
Measurement Error model estimate for correlation coefficient
MetaCyto: A package for meta-analysis of cytometry data.
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Network-Regularized Regression Models
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements from One Generation to the Next to a Treatment Effect
Predicting Targets for Drosophila Intragenic miRNAs
Predicting Targets for Drosophila Intragenic miRNAs
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Profile score distributions
Profile score distributions
Random Gene Set Enrichment Analysis
Random Gene Set Enrichment Analysis
Randomization routines for Clinical Trials
Randomization routines for Clinical Trials
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rcpp Integration Surrogate Variable Analysis
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNA-seq data analysis using the Poisson-Tweedie family of distributions
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
Rtreemix: Mutagenetic trees mixture models.
Rtreemix: Mutagenetic trees mixture models.
RUV for normalization of expression array data
RUV for normalization of expression array data
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Differential Expression
Somatic Signatures
Somatic Signatures
Somatic Signatures
SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results
SRGnet An R package for studying synergistic response genes from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data
Stability and Aggregation of ranked gene lists
Stability and Aggregation of ranked gene lists
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
Target Inhibition Interaction using Maximization and Minimization Averaging
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Uses Brown's method to combine p-values from dependent tests
Uses Brown's method to combine p-values from dependent tests
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Variance Adaptive Shrinkage
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis