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.
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 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 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.
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.
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.
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.
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 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 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 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.
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).
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.
Consists of a collection of investigation approaches and displays software for microarray data. Chipster is useful for several types of high throughput data such as microarrays, proteomics and next generation sequencing (NGS). It can be employed to normalize most of the commonly used chip types and permits to utilize the remapped information. This tool is useful for RNA degradation, relative log expression (RLE), normalized unscaled standard error (NUSE) or quality control probe expression.
Integrates data from different sources and experiments. CANEapp is a platform for integrating next-generation sequencing (NGS) analysis pipelines and tools into a user-friendly suite that can be immediately accessed by scientists. It utilizes a standardized analysis pipeline and internally generated experimental design templates. It allows users to work on NGS data and high-throughput data.
Integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions.
Performs quantification of expression on miRNA precursors and mature forms of miRNAs, and allows for discovering differentially expressed markers. miFRame is a software for the analysis of single miRNAs as well as miRNA sets from human next generation sequencing (NGS) data that can be easily applied by researchers. However, it also offers to discover potentially dys-regulated novel mature miRNAs, differentially regulated iso-miRNAs and performs a per-base expression analysis.
Focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. eRNA provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis.
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.
Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a selection of state-of-the-art RNA-seq tools and methods with minimal effort to run. This tool organizes computational results in reproducible, presentable, and easy-to-use formats for in-depth investigation.
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.
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.
Can quantify and analyze small non-coding RNA species (sncRNAs). Smallrnaseq allows general analysis of small RNAs and not just miRNAs. It can be integrated into another platform thank to the application programming interface (API) function. The tool is simple to use and may be attractive to users. It provides a comprehensive set of pipelines for automated analysis of high throughput sequencing data.
Annotates sncRNA. AASRA is based on a unique anchor alignment algorithm which avoids repetitive or ambiguous counting. It is able to differentiate mature miRNA from precursor miRNA reads. The tool is able to identify new sncRNA variants in the sncRNA-Seq sequencing reads. By using AARSA, users can reduce quantification bias, revisit their sncRNA data in order to underline how many variants were inadvertently excluded.
Aims to capture information inherent in the datasets. RAPID is a program able to produce numerous visualizations as user-friendly HTML reports, covering multiple categories required for sRNA analysis. It includes features for simplifying an automated comparison of multiple datasets and integrates differential expression analysis using DESeq2. Moreover, it can quantify the basic alignment statistics with respect to read length, strand bias, non-templated nucleotides, nucleotide content, or sequencing coverage.
Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq, MeDIP-seq and ChIP-seq experiments. This tool includes standard differential expression analysis for different experimental conditions, as well as differential splicing analysis. It can notice variants in the transcriptome and gene fusion events.
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.
Identifies sRNA loci on plant genomes from two sRNA datasets, which can be uploaded by the user or selected from publicly available datasets. SiLoCo maps sRNA sequences to the genome using PatMaN and weighs each sRNA hit by its repetitiveness in the genome. The method uses the normalised and weighted read-abundance and relative position of sRNAs on the reference genome to predict the sRNA loci.
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.
An automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform.
An easy to use perl-based analysis pipeline to handle sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. It reports the most commonly used results to the user in a comprehensive expression table and data visualization track files for the UCSC genome browser. Although successfully tested on chicken data, the pipeline can also be used to analyze miRNA data from any species. There are two versions of the E-miR pipeline, either implementing the Bowtie or Eland aligner.
A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.
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