Allows analysis of high-throughput small RNA data. UEA sRNA toolkit is a suite of interactive sRNA analysis tools, which provides a platform to create workflows for processing small RNA (sRNA) next generation sequencing (NGS) data. The software includes (1) helper tools, (2) computational analysis tools and (3) visualization tools. It permits users to combine workflows and stand-alone tools complemented with visualization features. UEA sRNA toolkit can assist in gaining an understanding of the sRNAome in plants and animals.
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.
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.
A pipeline to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance.
Allows to analyse, annotate, compare and visualize small RNA sequencing data. SPAR offers to users the possibility to streamline interpretation of small RNA-seq results and to compare with up to hundreds of publicly available datasets. This tool executes unsupervised segmentation to identify sncRNA loci displaying features of specific processing in the provided sequencing data. This pipeline is available through a web application and a standalone software.
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.
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.
Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in combining available tools, workflows and training material, as well as providing easy access for experimentalists. It serves as a central hub for programmers, which can easily integrate and deploy their existing or novel tools and workflows.
Identifies MicroRNAs (miRNA) in animals. miRdentify is a miRNA prediction strategy that, based on gradual increase in 10 parameters, ensures a selection of highly miRNA-like hairpin structures. The software predicts more than 400 novel human miRNAs including the first human male-specific miRNA, which was validated by northern blotting. Furthermore, it also predicted several novel miRNAs in the mouse, the fruit fly and nematodes.
Aims to reduce the efforts put into basic data processing for next-generation sequencing (NGS). QuickNGS enables data analysis for major applications of NGS in a batch-like operation mode. This pipeline relies on the organization of available metadata in a MySQL database which is used to control the overall workflow composed of specific software applications for different kinds of analysis.
Assists in understanding and analyzing microRNA sequencing data. miRge consists of a multiplexing method to align microRNAs (miRNAs) and other RNA species to expressed libraries. It includes among others miRNA annotation, A-to-I analysis, or miRNA detection. It uses both miRNA hairpin sequence structure and composition of isomiRs resulting in a more specific capture of potential miRNAs.
Allows users simultaneously perform mRNA and miRNA expression analysis. wapRNA is a web application that includes major processes for the next-generation mRNA or miRNA data analysis, including preprocessing raw sequenced reads, mapping tags to reference sequences, gene expression annotation, and other downstream functional analysis such as detecting differentially expressed genes, Gene Ontology and KEGG pathway analysis for RNA, novel miRNA predication and miRNA target prediction. Executable packages are available for users to build their pipeline locally.
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 consists of a didactical tool that can be employed to introduce scientists to the utilization and interpretation of microarray data. This tool serves in the investigation of microarray experiments based on the consolidated 3’ Affymetrix expression arrays.
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.
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.
Allows rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.
A pipeline designed to analyse RNA sequencing data by producing graphical and MySQL output. Nine different steps of analyses are possible, ranging from trimming to annotation or pattern search. The pipeline output includes graphical summaries, text files that can be easily parsed and automatic construction of a MySQL database, which allows simultaneous querying of expression and annotation data.
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.
A method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs). These sncdRNAs are often detected in sequencing data and observed as fragments of their precursor sncRNA. Using small RNA-seq read alignments, FlaiMapper is able to annotate fragments primarily by peak-detection on the start and end position densities followed by filtering and a reconstruction process.