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Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. It offers a comprehensive microarray analysis for Affymetrix 3′ (IVT) expression arrays as well as for the new generation of whole transcript arrays: human/mouse/rat exon 1.0 ST and human gene 1.0 ST arrays. oneChannelGUI inherits the core affylmGUI functionalities and permits a wider range of analysis allowing biologists to choose among different criteria and algorithms in order to analyze their data. It is a didactical tool since it could be used to introduce young life scientists to the use and interpretation of microarray data. For this purpose various data sets and exercises are available at the oneChannelGUI web site.


A collection of small RNA analysis tools. 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.

CPSS / Computational Platform for analysis of Small RNA deep Sequencing data

Provides a comprehensive integrated pipeline for analyzing small RNA deep sequencing data. CPSS delivers analysis report from ncRNA quantification to miRNA target prediction and annotation of single and multiple datasets. The webserver supports more than 40 species. Each detailed result pages include a search function to find specific terms or values. For Gene Ontology (GO), pathway and protein domain analysis, users can optimize parameters and rerun analysis at each detailed result page.

TRAPLINE / Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect protein-protein interactions (PPIs), miRNA targets and alternatively splicing variants or promoter enriched sites. This tool includes different modules for several functions: (1) it scans the list of differentially expressed genes; (2) it includes modules for miRNA target prediction; and (3) a module is implemented to identify verified interactions between proteins of significantly upregulated and downregulated mRNAs.


A free web service that allows to study short read data from small RNA-seq experiments. DARIO provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The expression data and ncRNA predictions can be downloaded in the standardized BED format. We provide a script to locally convert SAM files and other mapping files to the BED format. The script is optimized to greatly reduce the amount of data that has to be uploaded to the DARIO server.


Allows to analyse microRNA deep sequencing data. miRNAKey is designed to be used as a base station for the analysis of miRNA sequencing data. The main steps include: (i) searching for and removing the adaptor sequence from the 3 -ends of the reads; (ii) mapping the reads to known miRNA databases, (iii) counting reads mapped to the different miRNA species in each sample, and converting these counts into the normalized RPKM (Reads Per Kilobase Million) expression-index to allow comparison across experiments and (iv) quantifying differential expression for miRNAs between paired samples.

SoMART / Solanaceae miRNA/tasiRNA Analysis Resources and Tools

Helps users to characterize tasiRNA genes. SoMART is a web server that consists of four online tools and four types of databases. The tools include (i) Slicer detector, (ii) dRNA mapper, (iii) PreMIR detector and (iv) sRNA mapper. The databases includes (i) sRNA databases, (ii) filtered sRNA (fRNA) databases, (iii) degradome RNA (dRNA) databases and (iv) DNA databases from three Solanaceae species: Nicotiana tabacum (tobacco), Solanum tuberosum (potato) and Solanum lycopersicum (tomato).

ISRNA / Integrative Short Reads NAvigator

A piece of online software designed for storage, visualization and analysis of small RNA sequencing data produced by high-throughput sequencing technologies. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets.


Provides many basic features of a small RNA-seq analysis, including quality control, read normalization, short non-coding RNAs, particularly focused on plants. plantDARIO provides data for A. thaliana, B. vulgaris and S. lycopersicum. It is based on basic workflows to analyze small RNA-seq data. The user can obtain a comprehensive overview starting after read mapping. The tool allows to inspect analysis results quickly after uploading data thank to the utilization of pre-compiled sncRNA annotations.


Quantifies known miRNAs and predicts novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification.


An online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile. It allows the mapping of the input sequences to miRBase in order to decipher the miRNA expression content in the input samples. It also identifies any modifications related with the input sequences. The modification types that are being supported include all types of 3’-modifications (e.g. uridylation, adenylation, ADAR editing), 5’-modifications and also internal modifications (SNPs and ADARs). Chimira expects as an input FASTQ or FASTA files containing adapter and/or barcode stripped small RNA-Seq data.


A web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze 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 API 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. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data.


A web-based pipeline which can automatically identify and link validated miRNA target interactions (MTIs) from extensive lists of miRNAs and target genes in batch mode, even if the provided data is not species specific. LimiTT enables an automatic assignment of experimentally validated MTIs to a given set of miRNAs and possible targets (e.g. an annotated transcriptome or proteome). In order to permit application to niche model organisms, the tool is able to process species overlapping datasets which are compared to a wide range of MTIs collected from multiple MTI DBs. Furthermore, the pipeline comprises a method to consider ranked target lists to assess the potential influence of miRNAs on the phenotype under investigation by the determination of an enrichment score for miRNA target sets. LimiTT represents a valuable tool to rapidly scan large amounts of data from high throughput research to identify miRNA/target interactions without large investments in on-site computational hardware.


A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. QuickNGS considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.


A software pipeline for rapid processing and analysis of data from high-throughput miRNA sequencing experiments. Features of SMiRK include adaptor trimming, alignment, normalization, data visualization, and statistical analysis. The main advantage of SMiRK is that it performs analysis of data without requiring the dedicated efforts of a bioinformatician or statistician. Furthermore, its highly automated nature means that little human intervention is needed to direct the data analysis, but the program can still prove useful to skilled users who wish to use it as a tool set.

iSRAP / integrated Small RNA Analysis Pipeline

A one-touch integrated small RNA analysis pipeline (iSRAP) research tool that is composed of widely used tools for rapid profiling of small RNAs. The performance test of iSRAP using publicly and in-house available data sets shows its ability of comprehensive profiling of small RNAs of various classes, and analysis of differentially expressed small RNAs. The flexible and powerful features of iSRAP enable a comprehensive analysis of small RNAs, which covers from quality assessment of input data to differential expression analysis and visualization of results with the ease of use. iSRAP can potentially serve as a platform for rapid analysis of transcriptomic data so that a better-informed decision can be made on the downstream analyses.


Provides genomics and proteomics products and services for academic and governmental research institutes, pharmaceutical and biotechnology industry. Genecopoeia, Inc. is a US-based manufacturer that released into market the largest number of human full length protein coding open reading frame (ORF) cDNA clones in multiple sets of vector systems with various features which make these clones suitable for a variety of functional assays, protein expression and easy purification in many cell types as well as cell free transcription and translation coupling systems, and large scale functional genomics and proteomics studies.


A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.


Allows investigation of non-coding RNA (ncRNA) sequences, expression levels, differentially expressed ncRNAs and miRNA-targeted genes and their functional annotation. mirTools provides several modules including (1) a single case to detect various types of known and novel ncRNAs and perform functional annotation of the miRNA-targeted genes for a single sample, (2) two cases and group cases to identify differentially expressed ncRNAs between or among samples, and (3) re-analysis to run previously submitted data with adjustable parameters.


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An effective platform for the identification and the visualization of miRNAs and their cognate isomiRs using NGS datasets spanning 193 species (including plants, animals and viruses using miRbase v.19). isomiRex has been developed with the goal to find, annotate and intersect microRNAs from plant and animal NGS datasets on one platform with a single data submission. The web platform provides an effective way for the identification of the miRNAs in the NGS dataset and. simultaneously infers the differential expression of the identified miRNAs by taking into account all the sequence variants generated from miRNA precursors (pre-miRNA) along with indexed reference mature miRNA sequence. Moreover, isomiRex can be potentially exploited for the identification of isomiRs with higher copy number as compared to the selected reference mature miRNA in miRBase.