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CLASS – Splice Variant Annotation from RNA-Seq Reads

CLASS – Splice Variant Annotation from RNA-Seq Reads

Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to capture splicing variation accurately has proven difficult. Current programs find major isoforms of a gene but ...

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Disease Biomarker Query from RNA-Seq Data

Disease Biomarker Query from RNA-Seq Data

As a revolutionary way to unveil transcription, RNA-Seq technologies are challenging bioinformatics for its large data volumes and complexities. A large number of computational models have been proposed for differential expression (DE) analysis and normalization from different standing points. However, ...

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Newly aligned modENCODE RNA-Seq coverage data

Newly aligned modENCODE RNA-Seq coverage data

Sue Celniker’s group has provided FlyBase with updated RNA-Seq coverage data for the modENCODE transcriptome datasets. The high-throughput sequencing reads from these experiments have been re-aligned to the new BDGP Release 6 reference genome assembly (NCBI accession GCA_000001215.4). This update ...

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miRNA Temporal Analyzer (mirnaTA) – for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation

miRNA Temporal Analyzer (mirnaTA) – for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation

Many open-source bioinformatics tools to identify existing and/or discover novel miRNAs in next-generation sequencing (NGS) reads have become available. While miRNA identification and discovery tools are significantly improved, the development of miRNA differential expression analysis tools, especially in temporal studies, ...

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MeT-DB: a database of transcriptome methylation in mammalian cells

MeT-DB: a database of transcriptome methylation in mammalian cells

Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase is the first comprehensive resource for N6-methyladenosine (m6A) in mammalian transcriptome. It includes a database that records publicaly available data sets ...

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QuaCRS – An Integrated RNA-Seq Quality Control Pipeline

QuaCRS – An Integrated RNA-Seq Quality Control Pipeline

QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses ...

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