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amplicon

Statistics and visualization for amplicon data

bioinformatic-resources

caveearthworms

co-occurrence

R scripts for performing co-occurrence analyses

co-occurrence_network_analysis

R and python scripts for correlation-based network analysis

data_processing

process high throughput marker gene sequence data

earthnetwork

Microbial co-occurrence network inferred from Earth Microbiome Project

emp

Code repository of the Earth Microbiome Project.

epicon-drought-study

The following code was used in the analysis of data generated as part of a DOE funded project to explore the relationship between drought and microbial recruitment in Sorghum bicolor. # For detailed descriptions of experimental design, please see the associated publication. In brief, we planted two different sorghum cultivars (RTx430 and BTx642) within a randomized block design that accounted for treatments, genotypes and replication, with three replicate blocks in total. # From this field experiment, we collected a variety of plant phenotypes, soil measurements, and rhizosphere, root and soil samples for microbial community analysis and metatranscriptomics. # All samples were collected weekly at the same time of day (between 10am and 1pm) and the same day of the week for seventeen weeks following seedling emergence (TP1 to TP17).

foodwebs_env_variation_coexistence

Final code to accompany the manuscript "Quantifying the relative importance of competition, predation, and environmental variation for species coexistence"

frontiers-review-2015

fungi_biodiv_commassembly

This is code for analysis of biodiversity patterns and community assembly processes of fungal communities

ggcor-hou

ggcor备用源，版权归houyunhuang所有，本源仅供应急使用

ipv6-hosts

markerdb

Build sequence databases for commonly used marker genes :scroll:

markov

Uses Markov chains to generate speech/text which mimics input text

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

metagenome

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

nee_speciescoexistence

This code for 'Spatial scales of species coexistence' by Harte and Levin

nestedness.emp

Software for performing Earth Microbiome Project nestedness analyses.

paperrobot

Code for PaperRobot: Incremental Draft Generation of Scientific Ideas

personal-website

Code that'll help you kickstart a personal website that showcases your work as a software developer.

plant_co-occurrence_patterns

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

speciesdistributionmodeling

Software for mapping the geographic distributions of microbial taxa, genes, and traits using ecological niche modeling.

spider_python

python爬虫

stampa

Sequence Taxonomic Assignment by Massive Pairwise Alignments

vsearch

Versatile open-source tool for metagenomics