| # | Name | Description | Online/Local | Organism Specific |
Features | 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: 96 | ||
| 3 | CleaveLand4 | CleaveLand a generalizable computational pipeline for the detection of cleaved miRNA targets from degradome data. CleaveLand takes as input degradome sequences, small RNAs and an mRNA database and outputs small RNA targets. | / | Homepage Publication Nov. 18, 2008 Citations: 313 | ||
| 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: 25 | ||
| 5 | DARIO | A free web server for the analysis of short RNAs from high-throughput sequencing data. | / | Homepage Publication May 27, 2011 Citations: 34 | ||
| 6 | 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: 20 | ||
| 7 | 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: 11 | ||
| 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: 11 | ||
| 9 | IsomiRage | A workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRage permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms. | / | Homepage Publication Sept. 29, 2014 Citations: 40 | ||
| 10 | LeARN/smallA | A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. | / | Homepage Publication Jan. 14, 2008 Citations: 8 | ||
| 11 | miR-PREFeR | MiR-PREFeR uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | / | Homepage Publication June 14, 2014 Citations: 54 | ||
| 12 | miRA | miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. | / | Homepage Publication Nov. 5, 2015 Citations: 40 | ||
| 13 | miRDeep-P2 | miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. | / | Homepage Publication Dec. 6, 2018 | ||
| 14 | miRDeep2 | miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades | / | Homepage Publication Sept. 12, 2011 Citations: 1513 | ||
| 15 | miRdentify | A stringent approach to confidently predict novel miRNAs in animals. | / | Homepage Publication July 22, 2014 Citations: 8 | ||
| 16 | MIREAP | MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA library. | / | Homepage Publication | ||
| 17 | MIReNA | MIReNA looks for miRNA sequences by exploring a multidimensional space defined by only five (physical and combinatorial) parameters characterizing acceptable pre-miRNAs. MIReNA validates pre-miRNAs with high sensitivity and specificity, and detects new miRNAs by homology from known miRNAs or from deep sequencing data. | / | Homepage Publication June 30, 2010 Citations: 65 | ||
| 18 | miRExpress | A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. | / | Homepage Publication Oct. 12, 2009 Citations: 106 | ||
| 19 | miRNA Digger | miRNA Digger was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. | / | Homepage Publication Jan. 6, 2016 Citations: 8 | ||
| 20 | MIRPIPE | MIRPIPE represents a new pipeline for the quantification of microRNA based on smallRNA sequencing reads. In opposition to present algorithms that generally rely on genomic data to identify miRNAs, MIRPIPE focuses on niche model organisms that lack such information. Among the MIRPIPE features are automatic trimming and adapter removal of raw RNA-Seq reads originating from various sequencing instruments, clustering of isomiRs, and quantification of detected miRNAs by homology search versus public or user uploaded reference databases. | / | Homepage Publication Aug. 26, 2016 Citations: 11 | ||
| 21 | miRPlant | The objective of miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. | / | Homepage Publication Aug. 12, 2014 Citations: 40 | ||
| 22 | mirPRo | mirPRo is a tool for miRNA-seq analysis. It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. | / | Homepage Publication Oct. 5, 2015 Citations: 22 | ||
| 23 | miRSeqNovel | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. | / | Homepage Publication May 17, 2012 Citations: 7 | ||
| 24 | 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 | ||
| 25 | 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: 42 | ||
| 26 | ncPRO-seq | ncPRO-seq is a tool for annotation and profiling of ncRNAs using deep-sequencing data. This comprehensive and flexible ncRNA analysis pipeline, aims in interrogating and performing detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO-seq pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. | / | Homepage Publication Oct. 7, 2012 Citations: 51 | ||
| 27 | 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: 33 | ||
| 28 | 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: 31 | ||
| 29 | PIPmir | PIPmiR is a algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. The algorithm can be used as the full pipeline, as just a classifier, or as just a plant precursor sequence predictor. | / | Homepage Publication Sept. 22, 2011 Citations: 65 | ||
| 30 | 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 | ||
| 31 | Prost! | Prost! (PRocessing Of Short Transcripts) analyzes any source of smallRNA sequencing data. Prost! does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single Prost! run, allowing a more accurate analysis of an entire dataset. After grouping the processed reads by genomic location, Prost! then annotates the reads using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally Prost! contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the Prost! analysis are provided into the excel file output for the user to have all information in hands for deeper analysis of specific cases. | / | Homepage Publication March 8, 2019 Citations: 21 | ||
| 32 | QuagmiR | QuagmiR - the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designated for the detection and annotation of isomiRs of heterogeneous nature. It permits extensive customization of the query process and reference databases to meet the user’s diverse demands. QuagmiR is written in Python and can be obtained freely from Github. QuagmiR can be run from command-line on local machines, as well as high performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud. | / | Homepage Publication | ||
| 33 | 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 | ||
| 34 | SeqBuster | A command-line bioinformatic tool usefull for the analysis of deep sequencing data, namely known miRNAs and isomiRs annotation. | / | Homepage Publication Dec. 11, 2009 Citations: 108 | ||
| 35 | 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 | ||
| 36 | ShortStack | ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ‘clusters’ de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, and detailed text-based alignments of all MIRNAs. It can also be used to quantify a set of input loci with genomic coordinates determined a priori by the user. | / | Homepage Publication | ||
| 37 | sPARTA | A powerful tool for plant miRNA target prediction and PARE validation. It can search for targets in unannotated genomic regions, which is useful to discover novel regulatory modules, independent of genome annotations that may be incomplete. | / | Homepage Publication Aug. 12, 2014 Citations: 36 | ||
| 38 | 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: 118 | ||
| 39 | sRNAtools | sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes. | / | Homepage Publication Jan. 18, 2021 Citations: 21 | ||
| 40 | 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: 149 | ||
| 41 | 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 |
