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.1382 days ago
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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 Mise...is processed into the table of exact amplicon sequence variants (ASVs) present...g taxonomy and assigning species to sequence...1335 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 R...t Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon al...1334 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, avail...re web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded f...1321 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...SP can estimate several measures of DNA sequence variation within and between...1321 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 Contr...lacking a single TF in a particular neuronal subtype 4) Single cell RNAseq analysis of neurons divided by Immedia...1320 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...1296 days ago
Applied Computational Genomics Course at UU: Spring 2020
...l concepts and experimental approaches in the analysis and interpretation of experim...ncing technologies will be explored including sequence alignment, the identification...tructural variation, and ChIP-seq and RNA-seq analysis. Students will learn and appl...1293 days ago
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