Beast code in Giters

Hunter Seabolt's repositories

tautyping

This pipeline identifies genes or genomic segments which most closely resemble the genome-wide phylogenetic signal of a given organism using the Kendall Tau rank correlation statistic

Language:NextflowMIT2 1 7

metaXplore

A modular bioinformatics pipeline to conduct basic, rapid data exploration of metagenomic sequencing data at a glance.

Language:NextflowMIT1 1 1

nexus_utils

A collection of homebrew scripts for operating on Nexus-formatted biological sequence data

Language:PerlMIT1 10

phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

Language:PythonApache-2.0100

bioconda-recipes

Conda recipes for the bioconda channel.

Language:Shell000

genomeannotator

Pipeline for the identification of (coding) gene structures in draft genomes.

Language:NextflowMIT000

Gibbs

A Perl module implementing a Gibbs sampler

Language:PerlMIT010

HMM

A Perl implementation of Hidden Markov Models

Language:PerlMIT010

InformationTheory

Perl tools for information theory application and calculations

Language:PerlMIT010

KmerTK

A collection of bioinformatics scripts for operating with sets of k-mers derived from genome sequences.

Language:PerlMIT010

Kolander

highly flexible sequencing read sieve for taxonomic filtering of next-generation sequencing data.

Language:GroovyMIT010

Markov

A Perl implementation of discrete-time Markov chains

Language:PerlMIT010

matrix_power_tools

A command-line set of power tools for matrix operations, including data munging, resampling, statistics, information content, and linear algebra.

Language:PerlMIT010

MLST

A Perl module for multilocus sequence typing applications (MLST)

Language:PerlMIT010

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

Language:NextflowMIT000

mycosnp-nf

CDCgov/mycosnp-nf

Language:NextflowApache-2.0000

ProbabilityDistributions

Perl implementations of various common probability distributions for data science

Language:PerlMIT010

rankGenes

An old workflow for identifying genes whose phylogenetic signal closely matches that of WGS

010

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Language:NextflowMIT000

vectorborne_SIR

Repo for CSE8803 course project covering extensions to vectorborne disease compartment models

Language:Jupyter NotebookMIT020

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

Language:NextflowMIT000