DEWE for RNA-seq

Just found DEWE (Differential Expression Workflow Executor) for RNA-seq analysis.  This tool provides a GUI that runs RNA-seq alignment through differential expression analysis using the Tuxedo suite of tools and the Bioconductor R package edgeR.  Pre-cooked pipelines include the tools HISAT2 and Bowtie2 for alignment, StringTie, Ballgown, and edgeR.  Ballgown is an R package that provides results visualization of the analysis. You can download DEWE … Continue reading DEWE for RNA-seq

gnomAD Browser Beta for disease and population variant exploration

The gnomAD Browser (http://gnomad-beta.broadinstitute.org) is hosted by the Broad Institute and provides a clean interface for browsing human genome variations.  The site pulls from over 123K exome sequences and over 15K whole-genome sequences from disease-specific and population studies, including all of ExAC.  It provides variant information and population breakdown, along with tissue specific gene and isoform expression through linking out to GTEx.  While in the … Continue reading gnomAD Browser Beta for disease and population variant exploration

RNAseq Data Sources: Recount2 and ARCHS4

The recount2 R package provides RNA-seq count matrices for over 70,000 public RNA-seq experiments from TCGA, SRA, and GTEx databases.  Recount2 also contains various tools and methods for analysis of the data, including differential expression at the gene and exon level, enrichment analysis, genomic region visualization, and more.  The package is available through Bioconductor: http://bioconductor.org/help/workflows/recountWorkflow/ Another RNA-seq data source is ARCHS4: http://amp.pharm.mssm.edu/archs4/download.html   Continue reading RNAseq Data Sources: Recount2 and ARCHS4

Integrative analysis of RNA species – a new R package

A pre-print in BioRxiv of a new R package called GDCRNATools that enables one to perform an integrative analysis of RNA species from the GDC/TCGA data. GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan Ma, Jianming Lu, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia bioRxiv 229799; doi: https://doi.org/10.1101/229799 Continue reading Integrative analysis of RNA species – a new R package

Bioinformatics 101 to be broadcast live on Zoom!

The Bioinformatics 101 Seminar Series starts this week!  This year we will be providing live online access to the seminars via the Zoom conferencing system available here at VCU.  Additionally, lectures will be recorded for later viewing.  If you are working towards the certificate you must attend the sessions in person or view them live via Zoom for it to count as having attended.  Login … Continue reading Bioinformatics 101 to be broadcast live on Zoom!

The Data Refinery from the Childhood Cancer Data Lab

This is a potentially new resource for access to and analysis of childhood cancer data.  The Data Refinery at CCDL is supported through Alex’s Lemonade Stand Foundation. Presently, NIH’s Genomic Data Commons offers access to TARGET pediatric cancer data, but has limited analysis tools and features.  The Data Refinery aims to integrate and harmonize large scale data sets, including publicly available data such as that from … Continue reading The Data Refinery from the Childhood Cancer Data Lab

Bioinformatics 101 Seminar Series Fall 2017 – Registration Open!

  The C. Kenneth and Dianne Wright Center for Clinical and Translational Research (CCTR), is excited to bring back the Bioinformatics 101 Seminar Series!  This series introduces attendees to genomic bioinformatics concepts and applications, including the technology behind genomic high-throughput data, high-throughput sequencing analyses, and more. This year we will also discuss clinical and translational bioinformatics, their role in precision medicine, and will introduce a … Continue reading Bioinformatics 101 Seminar Series Fall 2017 – Registration Open!

SciLifeLab Metagenomics Workshop Docs

Came across this workshop material from 2014 on Metagenomics that give an introduction to metagenomic analyses, including metagenome assembly, comparative functional analysis, comparative taxonomic analysis, metagenomic binning and metagenomic annotation.  The tools have most likely been updated since the workshop, but it looks like a good place to branch out from if you are just starting in this area. SciLifeLab Metagenomics Workshop Continue reading SciLifeLab Metagenomics Workshop Docs

UALCAN – new TCGA analysis web-base tool

UALCAN is a new web-base tool to analyze TCGA gene expression data.  It includes gene expression heat maps, survival plots, and more for 31 TCGA cancer types. Note: UALCAN uses legacy TCGA data that has not been harmonized by GDC. Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK, Varambally S. (2017) UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and … Continue reading UALCAN – new TCGA analysis web-base tool