Jit
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Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2439 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...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1801 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...Encode sequencing data freely available to download and use for academic means
By Rahul Agarwal 3956 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 3716 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 3005 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...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2195 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...RNA-Seq Analysis: A Guide for Bioinformaticians
By LEGE 33 days agoRNA-Seq analysis is a cornerstone of modern transcriptomics, offering bioinformaticians a versatile toolkit for unraveling gene expression and regulation. Mastering RNA-Seq workflows and tools empowers researchers to transform raw sequencing data...dupRadar package
By Jit 2532 days agobioconductor.org - The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glanceDemo 4: Using BLAST/BLAT in Ensembl
By Radha Agarkar 4140 days agoWe demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in Ensembl, and identify hits to the genome, or to genes, with this tool.Genome Workbench 2.10.7
By Gudiya Pal 3115 days agoGenome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.
