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.1361 days ago
DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms
...d -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-se...s of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion para...1300 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
...bsp;Mining Algorithm for GenetIc Controllers (MAGIC),...enrichment of TFs and cofactors in gene bodies and flanking regions i...iori binary classification of genes as targets or non-targets. W...neurons divided by Immediate Early Gene expression levels. In summa...1300 days ago
1251 days ago
1242 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.1233 days ago
1206 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 identify...999 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression work...ified to the reference transcripts, and prepare gene-level count datasets for down...ationship between samples, perform differential gene expression analysis, and visu...983 days ago
914 days ago