Bioconductor Packages

Analysis of Alternative Splicing Using RNA-Seq

Add-on to CellNOptR: Discretized time treatments

ODE add-on to CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Reconstruction, visualization and analysis of branching trajectories

Coordinated Gene Activity in Pattern Sets

Methylation array and sequencing spatial analysis methods

Interactive Workflow for Discovering Rhythmicity in Biological Data

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

Visualise microarray and RNAseq data using gene ontology annotations

Gene Regulatory Network Inference Using Time Series

Calculate growth-rate inhibition (GR) metrics

Modeling RNA synthesis, processing and degradation with RNA-seq data

Functions used to analyze early tumor evolution from whole genome sequencing data

LiquidAssociation

Multi-Omics Simulation (MOSim)

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Soft clustering of omics time series data

An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

Maximum Likelihood Decay Modeling of RNA Degradation Data

Open-source toolkit to analyse data from xCELLigence System (RTCA)

R Normalization and Inference of Time Series data

RolDE: Robust longitudinal Differential Expression

Time course sequencing data analysis

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Breakpoint analysis of time-course expression data

Artificial Components Detection of Differentially Expressed Genes

GUI for limma Package with Affymetrix Microarrays

Bulk Linking Analysis for Single-cell Experiments

Clustering of Time Series Gene Expression data

Significance of periodic expression pattern in time-series data

Differential Expression Analysis for RNA-seq data through a robust variance component test

deltaGseg

Extraction of Differential Gene Expression

Empirical Analysis of Digital Gene Expression Data in R

Annotation and analysis of biological dynamical systems using flow cytometry

Linear Models for Microarray and Omics Data

GUI for limma Package With Two Color Microarrays

Significant Gene Expression Profile Differences in Time Course Gene Expression Data

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

mirTarRnaSeq

An R Package for Time Course RNASeq Data Analysis

Robust statistical inference for quantitative LC-MS proteomics

Fit Penalised Generalised Least Squares models

Rhythmicity Analysis Incorporating Non-parametric Methods

Rotation based gene set analysis

Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs, & GLMMs

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Transcription factor Inference through Gaussian process Reconstruction of Expression

Statistical Analysis for Developmental Microarray Time Course Data