1388 days ago
1378 days ago
G-NEST: The Gene NEighborhood Scoring Tool
The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.1345 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymo...several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-se..., as well as linkage disequilibrium, recombination, gene flo...1284 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...nrichment of TFs and cofactors in gene bodies and flanking regions i...ori binary classification of genes as targets or non-targets. W...eurons divided by Immediate Early Gene exp...1283 days ago
1235 days ago
1226 days ago
gggenomes: A grammar of graphics for comparative genomics
gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization packageggplot2 by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.1216 days ago
1190 days ago
WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identif...982 days ago