IsomiR detection software tools | Small RNA sequencing data analysis
Variants of microRNAs, called isomiRs, are commonly reported in small RNA sequencing. It is now possible to discern the overall complexity of miRNA populations that participate in gene regulatory networks.
Provides small RNA (smRNA) sequencing in human cancer research. YM500 not only focuses on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). YM500 contains more than 11000 cancer-related smRNA and 10000 RNA-seq datasets. YM500, through its web interface, allows users to: (i) search for small RNA expression, (ii) search for miRNA Isoform, (iii) search for Novel miRNA, (iv) search for miRNA’s arm switching, (v) drive meta-analysis, (vi) drive survival analysis, (vii) drive cancer analysis, (viii) download their results.
Permits users to analyse small RNA data from Illumina sequencing. SeqBuster is a web-based bioinformatic tool providing an automatized pre-analysis for sequence annotation. This software offers a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs. It contains an analysis module to explore the miRNA targets using the miRBase, PicTar and/or TargetScan algorithms.
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.
Allows to share and analyze aligned small RNA sequencing data. miRspring is a software document that aims to provide portability and a universal method to extract miRNA processing information from high-throughput sequencing (HTS) data sets. The software replicates the entire mapped data set and provides user-friendly way of presenting sequencing data along with inbuilt novel analysis tools that can globally assess the whole data set.
An online tool for detection and annotation of isomiRs from small RNA sequencing data. DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. DeAnnIso is able to handle the data from single, paired and group samples, and can complete the assigned job within 1 h, depending on data size, species and selected parameters for analysis.
Identifies templated and non-templated 5’-isomiRs and 3’-isomiRs. isomiR2Function allows the expression quantification using empirical bayes hierarchal model (EBSeq) and/or negative binomial distribution (DESeq). It permits to customize length range, seed corrupt tolerance and minimum sequencing depth for isomiR identification. The tool facilitates the large-scale discovery of isomiRs across the plant species.
A web platform to analyze expression pattern of miRNA at the miRNA/isomiR levels. miR-isomiRExp is based on the biological characteristics of miRNA and isomiR, it provides insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveals functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences.
Produces accurate miRNAs expression level quantification and both isomiRs and miRNA-mRNA interaction sites precise classification. isomiR-SEA exploits a miRNA specific alignment algorithm that is able to correlate the encountered mismatches with their positions on the miRNA sequence. It can be useful for analyses of large datasets. This tool allows users to design wide miRNAs studies.
Identifies and analyses non-templated nucleotide additions and trimming at both the termini of the miRNA sequences in sRNA next generation sequencing (NGS) data. miRMOD is a Windows-based standalone specialized package that provides useful statistics about various types of miRNA modifications along with its frequencies, differential miRNA-modified miRNA abundance and frequencies of the modified bases found in each of the modifications. It also analyses differences in miRNA target interactions, as a result of miRNA modifications.
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. IsomiRage is a standalone desktop application written in the Java programing language.
Detects miRNAs from smRNA-seq data, with an emphasis on separately annotating and quantifying functionally-distinct isoforms of canonical miRNAs, termed isomiRs. miRquant provides detailed information on the quality of the sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs (tRNA-derived RNAs) and yDRs (Y-RNA derived small RNAs), prevalence of post-transcriptional modifications such as A-to-I edits and 3’ non-templated nucleotide additions, and correlation in miRNA profiles across multiple samples. miRquant will be useful for researchers interested not only in quantifying known microRNAs but also mining the rich well of additional information embedded in small RNA-sequencing data.
Standardizes and automatizes the search for miRNAs isoforms in high-throughput small RNA sequencing libraries. isomiRID provides a tool to automate, standardize and simplify the searches for isomiRs and non-templated nucleotides in 3′ and 5′ miRNA ends, using as input single or multiple sequencing data files in a comparative way. The output files produced from this workflow are understandable tab delimited.txt files, which can be easily imported for spreadsheet or statistical suits, as R package. Also, the aligned output provides a broad view of particular miRNAs and the abundance of their isomiRs sequences in different sequencing datasets.
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.
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