Biocview "StatisticalMethod"

Adjust for positional and batch effects using ComBat
Adjust for positional and batch effects using ComBat
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Analysis of pooled genetic screens
Analysis of pooled genetic screens
Analyze Gene Sets Collections Properites
An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.
An R package for fast computing for adaptively weighted fisher's method
An R package for fast computing for adaptively weighted fisher's method
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
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Batch Effects Correction with Unknown Subtypes
Batch Effects Correction with Unknown Subtypes
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 profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Binomial Random Forest Feature Selection
Binomial Random Forest Feature Selection
Calculate and Visualize Synergy Scores for Drug Combinations
Calculate and Visualize Synergy Scores for Drug Combinations
Calculates Mulcom test
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Classes and methods for multi-omics data integration
Clonal ordering and visualization
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
CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Comparing Differential Abundance/Expression Methods
Compensates for the bias introduced by median normalization in phosphoproteomics
Concomitant identification of distinctness and similarity in gene expression analysis.
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
Controlling bias and inflation in association studies using the empirical null distribution
Correction of batch effects in DNA methylation data
Correction of batch effects in DNA methylation data
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Decomposition of individual tumors into mutational signatures by signature refitting
Decomposition of individual tumors into mutational signatures by signature refitting
DeMAND
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
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 novo deletion in targeted sequencing trios
Detection of de novo deletion in targeted sequencing trios
Detection of de novo deletion in targeted sequencing trios
Detect tissue heterogeneity in expression profiles with gene sets
Detect tissue heterogeneity in expression profiles with gene sets
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Different methods for the integrative analysis multiple omics data
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
distinct: a method for differential analyses via hierarchical permutation tests
Divergence Computations
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
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
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
FABIA: Factor Analysis for Bicluster Acquisition
Finding differentially expressed unannotated genomic regions from RNA-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
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
Functional similarities
Functional similarities
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences
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
Generate synthetic nucleosome maps
Generate synthetic nucleosome maps
Gene Set Analysis in R
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 with Networks
Gene Set Enrichment Analysis with Networks
genesis assocation testing code rewrite
genesis assocation testing code rewrite
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
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
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
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 of cancer cell lines based on their weighted mutational/ 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
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Integrated Differential Expression and Differential Network Analysis (INDEED)
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
interface to python sklearn via Rstudio reticulate
interface to python sklearn via Rstudio reticulate
interface to python sklearn via Rstudio reticulate
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Iteration removal method for feature selection
Iteration removal method for feature selection
Iterative Clustering
Iterative Clustering
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
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
Judging Quality of Clustering Methods using Mutual Information
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
MetaCyto: A package for meta-analysis of cytometry data
MetaCyto: A package for meta-analysis of cytometry data
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
Model based analysis for paired-end data
Model based analysis for paired-end data
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modified Concordance Index
Modified Concordance Index
Multiomic Batch effect Correction
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Neighbor_net analysis
Network Analysis Supported by Boosting
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
Network-based prioritization of putative metabolite IDs
Network Centrality Metrics for Elastic-Net Regularized Models
Network Centrality Metrics for Elastic-Net Regularized Models
Network-Regularized Regression Models
Network-Regularized Regression Models
Online error control
Online error control
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
PAIRADISE: Paired analysis of differential isoform expression
PAIRADISE: Paired analysis of differential isoform expression
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
Perform Chromosomal Ancestry Differences (CAnD) Analyses
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
PolyA counting and differential transcript usage analysis for scRNA-seq data
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Predict Combined Function of Transcription Factors
Predicting Targets for Drosophila Intragenic miRNAs
Predicting Targets for Drosophila Intragenic miRNAs
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
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
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Random Gene Set Enrichment Analysis
Randomization routines for Clinical Trials
Random Rotation Methods for High Dimensional Data with Batch Structure
Random Rotation Methods for High Dimensional Data with Batch Structure
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rcpp Integration Surrogate Variable Analysis
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
RNA-seq data analysis using the Poisson-Tweedie family of distributions
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust prediction of clinical outcomes using cytometry data without cell gating
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.
RUV for normalization of expression array data
Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies
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
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation
Selecting transcript model using PRO-seq
Selecting transcript model using PRO-seq
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Significance Analysis of Function and Expression
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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 to gene mutations from transcriptomics data
SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data
Stability and Aggregation of ranked gene lists
stageR: stage-wise analysis of high throughput gene expression data in R
stageR: stage-wise analysis of high throughput gene expression data in R
Statistical Analysis of MPRA data
Statistical Analysis of MPRA data
Statistical analysis of phenotypic data
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)
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
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
Subtype Identification with Survival Data
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
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"
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 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
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Tools for computing, querying and storing linkage-disequilibrium data
Transcript abundance linear modeling from compressed coverage information
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
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
XCI-inference
XCI-inference
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis