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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (637 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1093 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1254 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (1306 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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proActiv: Estimation of Promoter Activity from RNA-Seq data
By BioStar 2032 days agogithub.com - proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active...PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
By BioStar 2032 days agogithub.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins...
By BioStar 2032 days agoekhidna2.biocenter.helsinki.fi - PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for...SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
By BioStar 2032 days agogithub.com - SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them...GROMACS: a versatile package to perform molecular dynamics
By Neel 2038 days agohaddock.science.uu.nl - GROMACS is a versatile package to perform molecular dynamics, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and...PheWAS: R package is designed to provide an accessible interface to the phenome wide association...
By BioStar 2045 days agogithub.com - The PheWAS R package is designed to provide an accessible interface to the phenome wide association study. For a description of the methods available and some simple examples, please see the package vignette or the R documentation. For...WGDdetector: a pipeline for detecting whole genome duplication events using the genome or...
By LEGE 2053 days agogithub.com - WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis...wgd—simple command line tools for the analysis of ancient whole-genome duplications
By LEGE 2053 days agogithub.com - wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these...Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical...
By BioStar 2054 days agowww.sequenceontology.org - We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers...ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
By Jit 2062 days agogithub.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...
