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.1379 days ago
1348 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumina Mis...s processed into the table of exact amplicon sequence variants (ASVs) present...taxonomy and assigning species to sequences...1333 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Recip...rocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence...1332 days ago
vsFilt: A tool to improve virtual screening by structural filtration of docking poses
The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide ra...1319 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 polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from s...ware). DnaSP can estimate several measures of DNA sequence...1318 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...1318 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GP...ectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence...1294 days ago
Applied Computational Genomics Course at UU: Spring 2020
...bled by modern DNA sequencing technologies will be explored including sequence alignment, the identification...of genetic variation, structural variation, and ChIP-seq and RNA-seq analysis. Students will learn and apply...1291 days ago
1287 days ago