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RNA-seq workflow: gene-level exploratory analysis and differential expression
By Jit 1141 days agomaster.bioconductor.org - Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count...Tools for Differential expression analysis
By Abhi 746 days ago Comments (1)the sequenced reads can be mapped to the organism’s genes to assess how differently the genes are expressed under the experimental circumstances as opposed to the control scenario. This is known as differential expression (DE) analysisBioinformatician at work !!!
By Neel 3747 days agoThe busy life of a bioinformatician. Need many more hands to deal with additional job :)GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various...
By Rahul Nayak 2139 days agolce.biohpc.swmed.edu - GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information. It efficiently constructs gene...RNA-Seq Data Pathway and Gene-set Analysis Workflows
By Jit 4047 days agoDescribe the GAGE workflows on RNA-Seq data pathway analysis and gene-set analysis.Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2391 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1434 days agoamp.pharm.mssm.edu - With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface BioJupies now supports user accounts! Sign in from the top right corner of the page...Encode sequencing data freely available to download and use for academic means
By Rahul Agarwal 3908 days ago Comments (3)genome.ucsc.edu - In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed...deepTools
By Martin Jones 3668 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataLive Webinar on RNA-Seq Data Analysis on 9 Nov 2016
By Strand 2957 days agoLive Webinar on RNA-Seq Data Analysis Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical...
