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 Functional Approach To Impute Genetically Regulated Expression

A GAM based framework for analysis of ChIP-Seq data

Alikeness Based on Regression on Transciptome DECOnvolution

A mass spectrometry imaging toolbox for statistical analysis

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 Unbiased Splicing Pathway Analysis

An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

A pipeline for processing drug sensitivity screen data

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

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

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

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Breakpoint analysis of time-course expression data

Casc

Cell OrderiNg by FluorEScence Signal

Classification using generalized partial least squares

Clonogenic Survival Analysis in R made easy!

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

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

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 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

Construct nomograms for competing risk models

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Controlling bias and inflation in association studies using the empirical null distribution

Covariate Assisted Large-scale Multiple testing

Creating a DelayedMatrix of Regression Residuals

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 preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Delineate outstanding genomic zones of differential gene activity

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Develop and evaluate time series data models based on fluctuation based clustering

dgeAnalysis

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Differential Alternative Polyadenylation Analysis From Compositions

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 usage in immune repertoires

Differentially Expressed Gene-Gene pairs

Differentially Methylated Cytosines via a Bayesian Functional Approach

Discriminant Analysis for Evolutionary Inference

Empirical Analysis of Digital Gene Expression Data in R

Estimate Systems Immune Response from RNA-seq data

Exon-Intron Split Analysis (EISA) in R

Exposome and omic data associatin and integration analysis

Extraction of Differential Gene Expression

Fast and Interpretable Consensus Clustering via Minipatch Learning

Fast lasso-based isoform prediction as a flow problem

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Fit a Gamma-Poisson Generalized Linear Model

Fit Penalised Generalised Least Squares models

Fit transcriptional regulatory networks using gene expression, priors, machine learning

GEM: fast association study for the interplay of Gene, Environment and Methylation

GEne Network Inference with Ensemble of trees

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Analysis Using the Outcome of Differential Methylation

Gene Set Enrichment For ChIP-seq Peak Data

Gene-set Enrichment with Regularized Regression

Gene-Specific Phenotype EstimatoR

Genome wide association studies of multiple traits with Bayesian multilvel models

Genotype Imputed Gene Set Enrichment Analysis

genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)

Global Test for Counts

Global test for groups of variables via model comparisons

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

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

gwasurvivr: an R package for genome wide survival analysis

Hierarchical Inference

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Identification of genetic Variants affecting Alternative Splicing

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 tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Integrative analysis of Multi-omics data for Alternative Splicing

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

Logistic Factor Analysis for Categorical 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

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

mirTarRnaSeq

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

Multiview Intercellular SpaTial modeling framework

Negative binomial model for scRNA-seq

Negative Binomial Models to detect Differential Splicing

Network Centrality Metrics for Elastic-Net Regularized Models

Network-Regularized Regression Models

Normalization of Single-Cell mRNA Sequencing Data

Omics Data Integration Project

Omics Longitudinal Differential Analysis

Optimal p-value weighting with independent information

Outlier Protein and Phosphosite Target Identifier

PaIRKAT

Parallel Mixed Model

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

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

Prediction of gestational age with Illumina HumanMethylation450 data

Protein Micro Array Data Management and Interactive Visualization

Provides helper functions for microbiome preprocessing and analysis

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

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

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

Robust Inference for Absolute Abundance in Microbiome Analysis

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)

rqt: utilities for gene-level meta-analysis

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Simulation and Deconvolution of Omic Profiles

Smooth modeling of bisulfite sequencing

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Sparse Partial Correlations On Gene Expression

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data

Statistical analysis for the Colony Formation Assay

Statistical Analysis of High-Throughput Genetic Perturbation Screens

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 methods for analysing single cell RNA-seq data

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

Supervised mutational signatures

Switch-like differential expression across single-cell trajectories

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 Multi-Omics data integration

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for Metabolomics Data

Tools for Omics Data Analysis

Top Confident Effect Sizes

trajectory-based differential expression analysis for sequencing data

Transcriptional Data Guided fMRI Network Classification

Turn Bioconductor objects into tidy data frames

Unified statistal Modeling of Omics Data

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

Variance Stabilizing Transformation for Gamma-Poisson Models

xcore expression regulators inference

Biocview "Regression"

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