Rahul Nayak
A Bioinformatician
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PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
By Abhi 445 days agogithub.com - Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies,...
Libraries or management tools for high throughput sequencing data
Last updated 51 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...GA4GH Data Working Group
By Jitendra Prajapati 3171 days agohttp://ga4gh.org/#/ - GA4GH Data Working Group Led by David Haussler (UCSC) and Richard Durbin (Sanger Institute), the Data Working Group (DWG) of the Global Alliance brings together the leading Genome Institutes and Centers with IT industry leaders to create global...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2222 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...LRSDAY: Long-read Sequencing Data Analysis for Yeasts
By Poonam Mahapatra 1917 days agogithub.com - Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding...BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1435 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...Fundamentals of Data Visualization by Claus O. Wilke
By Abhi 169 days agoclauswilke.com - The book is meant as a guide to making visualizations that accurately reflect the data, tell a story, and look professional. It has grown out of my experience of working with students and postdocs in my laboratory on thousands of data...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2386 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...AccNET
By Jitendra Narayan 2970 days agosourceforge.net - AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET...NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
By Rahul Nayak 2336 days ago142.150.188.236 - NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output...
