Differential Expression AnalysisMethods for examination of miRNAs or their targets expression differences between given sets
| # | Name | Description | Online/Local | Organism Specific |
NGS Data Needed |
miRNA/mRNA differential expression |
Algorithm | References |
|---|---|---|---|---|---|---|---|---|
| 1 | BioVLAB-MMIA-NGS | BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. | / | / | Homepage Publication Sept. 29, 2014 Citations: 8 | |||
| 2 | CAP-miRSeq | Comprehensive analysis pipeline for deep microRNA sequencing (CAP-miRSeq) integrates read preprocessing, alignment, mature/precursor/novel miRNA qualification, variant detection in miRNA coding region, and flexible differential expression between experimental conditions. According to computational infrastructures, users can run samples sequentially or in parallel for fast processing. In either a case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. | / | / | Homepage Publication June 3, 2014 Citations: 88 | |||
| 3 | Chimira | Chimira is a web-based system for miRNA analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications, 5′-modifications and also internal modifications or variation. | / | / | Homepage Publication June 20, 2015 Citations: 60 | |||
| 4 | CPSS | CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. | / | / | Homepage Publication May 9, 2012 Citations: 23 | |||
| 5 | DeAnnIso | DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. | / | / | Homepage Publication May 13, 2016 Citations: 19 | |||
| 6 | eRNA | eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. | / | / | Homepage Publication March 5, 2014 Citations: 10 | |||
| 7 | iMir | iMir is a modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. | / | / | Homepage Publication Dec. 13, 2013 Citations: 26 | |||
| 8 | isomiR2Function | somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. | / | / | Homepage Publication March 21, 2017 Citations: 9 | |||
| 9 | isomiReX | IsomiRex is a open-access web platform to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. | / | / | Homepage Publication July 4, 2013 Citations: 25 | |||
| 10 | MAGI | MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. | / | / | Homepage Publication June 6, 2014 Citations: 10 | |||
| 11 | miRanalyzer | miRanalyzer – a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. | / | / | Homepage Publication April 22, 2011 Citations: 138 | |||
| 12 | miRNAkey | miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. It implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple mapping levels, generating a novel platform for the analysis of miRNA expression. The tabular and graphical output contains detailed reports on the sequence reads and provides an accurate picture of the differentially expressed miRNAs in paired samples. | / | / | Homepage Publication Aug. 27, 2010 Citations: 41 | |||
| 13 | mirnaTA | mirnaTA is an open-source, bioinformatics tool to aid scientists in identifying differentially expressed miRNAs which could be further mined for biological significance. | / | / | Homepage Publication Oct. 13, 2014 Citations: 7 | |||
| 14 | miRNet | miRNet is an easy-to-use web-based tool with comprehensive supports for statistical analysis and functional interpretation of various datasets generated in miRNAs studies. Users can explore the results in miRNA-target interaction networks with powerful features to assist in biological understanding. | / | / | Homepage Publication April 21, 2016 Citations: 199 | |||
| 15 | miRSeqNovel | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. | / | / | Homepage Publication May 17, 2012 Citations: 7 | |||
| 16 | mirTools 2.0 | MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. | / | / | Homepage Publication May 29, 2013 Citations: 40 | |||
| 17 | MMIA | MMIA integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions by Gene Set Enrichment Analysis. To assign biological relevance to the integrated microRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including various disease-associated genes as well as conventional canonical pathways and Gene Ontology. This novel web server provides users with miRNA-mRNA expression data combined analysis tools and broad gene sets. | / | / | Homepage Publication May 6, 2009 Citations: 87 | |||
| 18 | MTide | MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. | / | / | Homepage Publication Sept. 24, 2014 Citations: 36 | |||
| 19 | Oasis 2.0 | Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. | / | / | Homepage Publication Feb. 19, 2015 Citations: 31 | |||
| 20 | Omics Pipe | A computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. | / | / | Homepage Publication Jan. 30, 2015 Citations: 28 | |||
| 21 | plantDARIO | plantDARIO is a free web service focussing on the analysis of short-read data from small RNA-seq experiments in plants. It provides basic features including quality control, read normalization, ncRNA quantification, and prediction of putative novel ncRNAs. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. | / | / | Homepage Publication Dec. 23, 2014 Citations: 6 | |||
| 22 | RandA | RandA is a tool for deep-sequencing data analysis. It performs various RNA-seq analysis steps including: adapter clipping; alignment against a database derived from Rfam; multiple mapping handling; read count normalization and differential expression testing for each transcript detected in the samples. | / | / | Homepage Publication March 9, 2012 Citations: 9 | |||
| 23 | shortran | Shortran provides an efficient and user-friendly tool for flexible analysis of sRNA-seq data. Using shortran, user is able to quickly generate and combine annotation and profiling information from a complex sRNA-seq experiment. | / | / | Homepage Publication Aug. 22, 2012 Citations: 9 | |||
| 24 | sRNAtoolbox | sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. | / | / | Homepage Publication May 27, 2015 Citations: 108 | |||
| 25 | UEA sRNA Workbench | The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. | / | / | Homepage Publication May 24, 2012 Citations: 138 | |||
| 26 | wapRNA | wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on. | / | / | Homepage Publication Sept. 6, 2011 Citations: 26 |