The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone.
Complex designs are common in (observational) clinical studies. Sequencing data for such studies are produced more and more often, implying challenges for the analysis, such as excess of zeros, presence of random effects and multi-parameter inference. Moreover, when sample sizes are small, inference is likely to be too liberal when, in a Bayesian setting, applying a non-appropriate prior or to lack power when not carefully borrowing information across features.
High-throughput measurement technologies have triggered a rise in large-scale cancer studies containing multiple levels of molecular data. While there are a number of efficient methods to analyze individual data types, there are far less that enhance data interpretation after analysis. We present the R package Director, a dynamic visualization approach to linking and interrogating multiple levels of molecular data after analysis for clinically meaningful, actionable insights.
This report describes the miRQuest - a novel middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification that use different programming languages and methods to realize this task. It is difficult to understand each tool and apply it to diverse datasets and organisms available for miRNA analysis. miRQuest can easily be used by biologists and researchers with limited experience with bioinformatics.
Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions.
We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis--the analysis of 3' modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online.
Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available.
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014.
Our database aim to make it easy for researchers to find the right tools or data source for their own specific study in miRNA field. Now we have collect >1000 tools. This database will update when every new 100 tools add in. Last update time 22nd April, 2018 (v1.2).
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