surh

scip_barplot

Workshop materials for SFSU SCIP 2022.

pbi

Microbiome analysis for phosphate-defense interaction

AMOR

Abundance Matrix Operations in R

grins

Code for the manuscript describing discovery and distribution of GRINS in bacteria.

HMVAR

Human Microbiome Variant Analysis in R

Rmarkdown_workshop

SeqTools

Sequence utilities

wheelP

Designing synthetic bacterial communities for predictable plant phenotypes

alnnotator

Annotate multiple sequence alignments with domain information

Anchurus

Analyzing SNPs in metagenomes

ANCOM

R scripts for Analysis of Composition of Microbiomes (ANCOM).

awesome-selfhosted

A list of Free Software network services and web applications which can be hosted locally. Selfhosting is the process of hosting and managing applications instead of renting from Software-as-a-Service providers

checkm_batch

crn

Analysis of community reaction norms

hct

HGTector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

inStrain

Bioinformatics program inStrain

maia-chess

Maia is a human-like neural network chess engine trained on millions of human games.

micropopgen

Scripts and utilities used @TheFraserLab

mSel

Selection in microbiomes

nextflow-patterns

General nextflow patterns. Inspired by https://github.com/nextflow-io/patterns but more specific

phylomut

RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

run_roary

Run roary from a set of genbank files

sdm_useless_biology

simple-icons

SVG icons for popular brands

SLiM

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

syneco_sims

Diverse simulations for syncom design

utils

General utilities

vibrio_squid

Mathematical model(s) for the symbisis between Allivibrio fisheri and Euprymna scalopes