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core-phylogenomics

Pipeline for identifying core SNPs and building a phylogenetic tree

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

covid_data_science_misc

Data science scripts on COVID related things

cutadapt

cutadapt removes adapter sequences from sequencing reads

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

datasciencecoursera

datasharing

The Leek group guide to data sharing

decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

eg_minion_2016

Edinburgh Genomics MinION training 2016

ete

ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of any type of hierarchical trees. This includes phylogenetic trees, clustering results and profile-based trees. It supports node annotation, programatic tree drawing, circular visualization, SVG, PNG and PDF image rendering, and more!

f1000_workflow

fantaxtic

Fantaxtic plots for phyloseq objects!

ffq

A tool to find sequencing data and metadata from public databases.

fishtaco

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts

funannotate

Eukaryotic Genome Annotation Pipeline

gas_scripts_reference

Scripts and reference files to type Group A Streptococcus

genome-scripts

Genome Scripts used in fungal comparative genomics

genomics-data-index

Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.

genstats

Statistics course for JHU Genomic Data Science Sequence

gevitanalysisrelease

A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT

ggplot2

An implementation of the Grammar of Graphics in R

git-demo

A very quick demo of Git for beginners

glmmadmb

generalized linear mixed models with AD Model Builder

graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

hero

Highways Enumerated by Recombination Observations

hwglabr2

Collection of R functions used in the Hochwagen Lab

illuminati

scripts to automate illumina secondary analysis pipeline

insilico_pcr

extract long read subsequences from a pair of primers