Jit
Enthusiast computational biologist with business dream !!!
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kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2616 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...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2222 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...Kallisto vs Salmon: Choosing the Right Tool for RNA-Seq Quantification
By BioStar 309 days agoIn the world of transcriptomics, quantifying gene and transcript expression accurately and efficiently is crucial. With the explosion of RNA-Seq data, researchers have turned to fast, alignment-free tools that streamline the quantification process...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 2826 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...Mesquite: A modular system for evolutionary analysis
By Rahul Nayak 3154 days agogithub.com - Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics,...RNA-Seq Data Pathway and Gene-set Analysis Workflows
By Jit 4516 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 2860 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 1903 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...New RNA Seq tool
By Rahul Agarwal 4334 days ago Comments (4)www.genengnews.com - "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy." Tool...A 3D Map of the Human Genome
By Jitendra Narayan 4102 days agoSuhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand,...
