Jit
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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
By Jit 2470 days agohttp://etetoolkit.org - ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and...LRSDAY: Long-read Sequencing Data Analysis for Yeasts
By Poonam Mahapatra 1916 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...
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 2574 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2542 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...
Sample bandage input file for visual analysis
By Jit 1418 days agoSample bandage input file for visual analysis ...Powerful books for learning data analysis with R
By LEGE 180 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
By Jit 2266 days agowww.bioinformatics.babraham.ac.uk - SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1741 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...PLAR: Pipeline for lncRNA annotation from RNA-seq data
By Abhi 1052 days agowww.weizmann.ac.il - Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs...
