Biocview "Regression"

A collection of tools for imaging MS data processing
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A DownStream Chemo-Proteomics Analysis Pipeline
A Functional Approach To Impute Genetically Regulated Expression
A Functional Approach To Impute Genetically Regulated Expression
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
Alikeness Based on Regression on Transciptome DECOnvolution
Alikeness Based on Regression on Transciptome DECOnvolution
A mass spectrometry imaging toolbox for statistical analysis
Analyze flow cytometer data to determine sample ploidy
Analyze flow cytometer data to determine sample ploidy
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Association analysis of CNVs and imputed SNPs incorporating uncertainty
A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
A tool for quantification of associations between genotypes and phenotypes in genome wide association studies (GWAS) with Bayesian inference and statistical learning
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Breakpoint analysis of time-course expression data
Breakpoint analysis of time-course expression data
Casc
Cell OrderiNg by FluorEScence Signal
Classification using generalized partial least squares
Classification using generalized partial least squares
CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Companion package to chipenrich
Companion package to chipenrich
Comparing Differential Abundance/Expression Methods
Comprehensive Annotation of Predictive Features for Interval-based Genomic Data
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Confounding Explorer
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Controlling bias and inflation in association studies using the empirical null distribution
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Creating a DelayedMatrix of Regression Residuals
Creating a DelayedMatrix of Regression Residuals
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
csSAM - cell-specific Significance Analysis of Microarrays
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
dgeAnalysis
dgeAnalysis
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential cell type change analysis using Logistic/linear Regression
Differential cell-type-specific allelic imbalance
Differential Epigenetic Coregulation Test
Differential Expression Analysis for RNA-seq data through a robust variance component test
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene usage in immune repertoires
Differential gene usage in immune repertoires
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Cytosines via a Bayesian Functional Approach
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Exon-Intron Split Analysis (EISA) in R
Exon-Intron Split Analysis (EISA) in R
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Fast lasso-based isoform prediction as a flow problem
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Fit a Gamma-Poisson Generalized Linear Model
Fit a Gamma-Poisson Generalized Linear Model
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Gene set analysis following differential expression using linear (mixed) modeling with dream
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Enrichment For ChIP-seq Peak Data
Gene-set Enrichment with Regularized Regression
Gene-set Enrichment with Regularized Regression
Gene-Specific Phenotype EstimatoR
Gene-Specific Phenotype EstimatoR
Genome wide association studies of multiple traits with Bayesian multilvel models
Genome wide association studies of multiple traits with Bayesian multilvel models
Genome wide association studies of multiple traits with Bayesian multilvel models
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
Global Test for Counts
Global Test for Counts
Global test for groups of variables via model comparisons
Global test for groups of variables via model comparisons
Graphical Exploration of Design Matrices
Graphical Exploration of Design Matrices
GUI for limma Package with Affymetrix Microarrays
GUI for limma Package With Two Color Microarrays
GWAS-based Mendelian Randomization and Path Analyses
GWAS-based Mendelian Randomization and Path Analyses
gwasurvivr: an R package for genome wide survival analysis
gwasurvivr: an R package for genome wide survival analysis
gwasurvivr: an R package for genome wide survival analysis
Hierarchical Inference
Hierarchical Inference
Identification of genetic Variants affecting Alternative Splicing
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
immunological Elastic-Net model, implementation and optimization
Inference of gene regulatory networks from gene expression data
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Kernel-Based Analysis Of Biological Sequences
LEA: an R package for Landscape and Ecological Association Studies
Linear Models for Microarray Data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
MoPS - Model-based Periodicity Screening
Multilevel Model for Multivariate Responses with Missing Values
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression
Negative binomial model for scRNA-seq
Negative binomial model for scRNA-seq
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Network Centrality Metrics for Elastic-Net Regularized Models
Network Centrality Metrics for Elastic-Net Regularized Models
Network-Regularized Regression Models
Normalization of Single-Cell mRNA Sequencing Data
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
Omics Longitudinal Differential Analysis
Omics Longitudinal Differential Analysis
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
Outlier Protein and Phosphosite Target Identifier
Outlier Protein and Phosphosite Target Identifier
Parallel Mixed Model
Pathway Enrichment Based on Differential Causal Effects
Pathway Enrichment Based on Differential Causal Effects
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression
pinnacle: Gene set enrichment analysis based on genomic intervals
Prediction of gestational age with Illumina HumanMethylation450 data
Prediction of gestational age with Illumina HumanMethylation450 data
Prediction of gestational age with Illumina HumanMethylation450 data
Provides helper functions for microbiome preprocessing and analysis
Quality control and analysis tools for Illumina DNA methylation BeadChip
Quality control and analysis tools for Illumina DNA methylation BeadChip
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Regression Models with Multivariate Outcomes for Mass Cytometry Experiments
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
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust prediction of clinical outcomes using cytometry data without cell gating
Robust statistical inference for quantitative LC-MS proteomics
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
rqt: utilities for gene-level meta-analysis
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Smooth modeling of bisulfite sequencing
SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
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
Statistical analysis for the Colony Formation Assay
Statistical analysis for the Colony Formation Assay
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical Analysis of High-Throughput Genetic Perturbation Screens
Statistical analysis of RNA editing sites and hyper-editing regions
Statistical analysis of RNA editing sites and hyper-editing regions
Statistical Analysis of the GeneChip
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
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
Supervised mutational signatures
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
The data package associated with the MAGAR R-package
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Tools for matrices with precision weights, test and explore weighted or sparse data
Tools for matrices with precision weights, test and explore weighted or sparse data
Top Confident Effect Sizes
Top Confident Effect Sizes
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Transcriptional Data Guided fMRI Network Classification
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Variable Selection in Finite Mixture of AFT Regression and FMR
Variable Selection in Finite Mixture of AFT Regression and FMR