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Time-course analysis software tools | RNA sequencing data

Dynamic expression data, nowadays obtained using high-throughput RNA sequencing, are essential to monitor transient gene expression changes and to study the dynamics of their transcriptional activity in the cell or response to stimuli. Several…
maSigPro
Desktop

maSigPro

Allows the analysis of multiple time course transcriptomics data. maSigPro is a…

Allows the analysis of multiple time course transcriptomics data. maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between…

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ImpulseDE
Desktop

ImpulseDE

Captures single impulse-like progression patterns in high throughput time…

Captures single impulse-like progression patterns in high throughput time series datasets. ImpulseDE can be applied on any kind of high throughput gene expression data. It reports differentially…

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diffsplicing
Desktop

diffsplicing

A method for ranking the genes and transcripts according to the temporal change…

A method for ranking the genes and transcripts according to the temporal change they show in their expression levels. In order to identify differential splicing and its underlying dynamics, we model…

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CATchUP
Dataset

CATchUP

Provides information on spatiotemporal specific gene expression for eight plant…

Provides information on spatiotemporal specific gene expression for eight plant species. CATchUP provides information on approximately 70000 transcripts including the δdmax values, functional…

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EBSeq-HMM
Desktop

EBSeq-HMM

Recognizes genes with non-constant expression over multiple ordered conditions,…

Recognizes genes with non-constant expression over multiple ordered conditions, and simultaneously classify them into expression paths. EBSeq-HMM is based on an empirical Bayes mixture modeling…

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timeSeq
Desktop

timeSeq

Detectes the differentially expressed (DE) genes in time course RNA-Seq data.…

Detectes the differentially expressed (DE) genes in time course RNA-Seq data. The negative binomial mixed-effect model (NBMM) method is applied to gene expression data on a gene-by-gene basis. A…

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DICEseq
Desktop

DICEseq Dynamic Isoform spliCing Estimator via sequencing data

Determines the dynamics of the splicing isoform proportions from time series…

Determines the dynamics of the splicing isoform proportions from time series RNA-seq data. DICEseq is able to explicitly model correlations between different RNA-seq experiments. It aims to assist…

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TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

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Trendy
Desktop

Trendy

Analyzes expression dynamics in high throughput profiling experiments with…

Analyzes expression dynamics in high throughput profiling experiments with ordered conditions. Trendy provides statistical analyses and summaries of feature-specific and global expression dynamics.…

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Dynamic-BM
Dataset

Dynamic-BM Dynamic-BodyMap

Allows to find data about temporal gene expression profiles. The Dynamic-BM…

Allows to find data about temporal gene expression profiles. The Dynamic-BM interface is design in order to simplify the utilization by users for browsing and searching the dynamic expression pattern…

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FunPat
Desktop

FunPat

An R package for time series RNA sequencing data that integrates gene…

An R package for time series RNA sequencing data that integrates gene selection, clustering and functional annotation into a single framework. FunPat exploits functional annotations by performing for…

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DyNB
Desktop

DyNB

Allows to analyze RNA-seq time series data. DyNB is a statistical method built…

Allows to analyze RNA-seq time series data. DyNB is a statistical method built on the negative binomial likelihood and Gaussian processes (GPs). The software can be used to study relative…

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LIGAP
Desktop

LIGAP

Allows integrative analysis and visualization of multiple lineages over whole…

Allows integrative analysis and visualization of multiple lineages over whole time-course profiles. LIGAP is a computational methodology that is widely applicable to quantify differential time-course…

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edgeR
Desktop

edgeR empirical analysis of DGE in R

Allows differential expression analysis of digital gene expression data. edgeR…

Allows differential expression analysis of digital gene expression data. edgeR implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes…

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