RNA-Seq Blog Transcriptome Research & Industry News
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological...
Read More »MATQ_Drop – Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets
IMMUcan scDB – a fully integrated scRNA-seq database exclusively dedicated to human cancer
The development of single cell RNA-sequencing (scRNA-seq) technologies has greatly contributed to deciphering the tumor microenvironment (TME). An enormous amount of independent scRNA-seq studies have been published representing a valuable resource that provides opportunities for meta-analysis studies. However, the massive ...
Read More »Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data
Effective dimension reduction is essential for single cell RNA-seq (scRNAseq) analysis. Principal component analysis (PCA) is widely used, but requires continuous, normally-distributed data; therefore...
Read More »ESPRESSO – robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data
Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing...
Read More »L-RAPiT: Long Read Analysis Pipeline for Transcriptomics
L-RAPiT: Long Read Analysis Pipeline for Transcriptomics is an easy-to-use publicly available pipeline which allows for analysis of long read RNA-sequencing data within a cloud environment; namely, Google Colaboratory. L-RAPiT is available at the following address: https://github.com/Theo-Nelson/long-read-sequencing-pipeline Citation: Nelson, T.M.; ...
Read More »A new sequencing technique achieves high-quality results from small volumes of frozen tumor specimens archived in biobanks
Columbia researchers invent a technique to study cancer tissues archived in biobanks, increasing the number and variety of tumor samples available for scientific analysis and advancing the discovery of...
Read More »scRNAseq_KNIME workflow – a customizable, locally executable, interactive and automated KNIME workflow for single-cell RNA seq
Single-cell RNA sequencing (scRNA-seq) is nowadays widely used to measure gene expression in individual cells, but meaningful biological interpretation of the generated scRNA-seq data remains a...
Read More »Researchers produce first-ever toolkit for RNA sequencing analysis using a ‘pantranscriptome’
Analyzing a person’s gene expression requires mapping their RNA landscape to a standard reference to gain insight into the degree to which...
Read More »SAMStat 2 – quality control for next generation sequencing data
SAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and...
Read More »MARVEL – an integrated alternative splicing analysis platform for single-cell RNA sequencing data
Alternative splicing is an important source of heterogeneity underlying gene expression between individual cells but remains an understudied area due to the paucity of computational tools to analyze...
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