Data Analysis

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are ...
Venice: a non-parametric test for finding marker genes in single-cell RNA-seq data

To find marker genes in single-cell RNA-seq data, many popular methods now follow a common approach ...
rFASTCORMICS (RNASeq) – Identifying and targeting cancer-specific metabolism using network-based drug target prediction

A novel computer algorithm allows researchers to evaluate drugs’ effects and find new targets using ...
Scanorama – integration of heterogeneous single-cell transcriptomes

Integration of single-cell RNA sequencing (scRNA-seq) data from multiple experiments, laboratories a...
pcaExplorer – interactive and reproducible exploration of Principal Components for RNA-seq data

RNA-sequencing has become the standard experimental approach for accurately profiling the transcript...

scruff – an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

June 18, 2019 Leave a comment 1,391 Views

Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode identification or unique molecular identifier (UMI) deconvolution are necessary for preprocessing of data from ...

New single-cell RNA-Seq analysis pipeline available

June 18, 2019 Leave a comment 1,775 Views

Researchers at the Mount Sinai Health System have created an automated script that takes your raw files from cell ranger and creates an integrated clustered Seurat object that can be used for visualization and downstream analysis. The clustering pipeline available ...

3D RNA-seq – a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

June 12, 2019 Leave a comment 1,675 Views

RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on skilled bioinformaticians to perform...

Ryūtō – network-flow based transcriptome reconstruction

June 6, 2019 Leave a comment 1,129 Views

The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA...

RNAmod – an integrated system for the annotation of mRNA modifications

June 4, 2019 Leave a comment 1,000 Views

Dynamic and reversible RNA modifications such as N6-methyladenosine (m6A) can play important roles in regulating messenger RNA (mRNA) splicing, export, stability and translation. Defective mRNA modification through altered expression of the methyltransferase and/or demethylases results in developmental defects and cancer ...

CoCo – RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

May 31, 2019 Leave a comment 1,070 Views

Next generation sequencing techiques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Here ...

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RNA-Seq Blog Transcriptome Research & Industry News

Data Analysis

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

Venice: a non-parametric test for finding marker genes in single-cell RNA-seq data

rFASTCORMICS (RNASeq) – Identifying and targeting cancer-specific metabolism using network-based drug target prediction

Scanorama – integration of heterogeneous single-cell transcriptomes

pcaExplorer – interactive and reproducible exploration of Principal Components for RNA-seq data

scruff – an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

New single-cell RNA-Seq analysis pipeline available

3D RNA-seq – a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

Ryūtō – network-flow based transcriptome reconstruction

RNAmod – an integrated system for the annotation of mRNA modifications

CoCo – RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

quanTIseq – estimate the fractions of ten different immune cell types from RNA-Seq data

RNA sequencing integration into CellMiner and CellMiner CDB

Atlas of RNA sequencing profiles for normal human tissues

New computational tool enables powerful molecular analysis of biomedical tissue samples

A single-cell transcriptomic atlas of human neocortical development

RAGE-Seq – A genomic barcode tracker for immune cells

A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data

Invitae now using supplemental RNA analysis to enhance genetic variant interpretation in cancer testing

Columbia University: Two open post-doc positions for RNA-seq/spatial analyses in human brain disease

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

Researchers create a human liver cell atlas using single-cell RNA-Seq

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments