Tags: GeNeCK, gene, regulatory, network, construction, expression
1951 days ago
Tags: HGTector, automated, method, facilitating, genome-wide, discovery, putative, horizontal, gene, transfers
1946 days ago
gggenes: a ggplot2 extension for drawing gene arrow maps.
Install the stable version of gggenes from CRAN: install.packages("gggenes") If you want the development version, install it from GitHub: devtools::install_github("wilkox/gggenes") More at https://github.com/wilkox/gggenesTags: gggenes, ggplot2, extension, drawing, gene, arrow, maps
1447 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
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 prokaryotes. https://www.mdpi.com/2073-4425/11/7/756/htm https://shadowcaster.r...Tags: ShadowCaster, hybrid, approach, detection, horizontal, gene, transfer, prokaryotes, HGT
1406 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
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 on performing a all-vs-all sequence comparison,...Tags: PyParanoid, pipeline, rapid, identification, homologous, gene, families, set, genomes
1375 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as...Tags: MAGIC, tool, predicting, transcription, factors, cofactors, driving, gene, sets, ENCODE, data
1270 days ago
Tags: MetaEuk, sensitive, high-throughput, gene, discovery, annotation, large-scale, eukaryotic, metagenomics
1222 days ago
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://gi...Tags: GenomeQC, quality, assessment, tool, genome, assemblies, gene, structure, annotations
732 days ago
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more details and practical considerations for running&n...Tags: homologizer, Phylogenetic, phasing, gene, copies, polyploid, subgenomes
351 days ago
OMArk: software for proteome (protein-coding gene repertoire) quality assessment
OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk reli...Tags: OMArk, software, proteome, protein-coding, gene, repertoire, quality, assessment
88 days ago