junqiangzheng Goto Github PK

16s-main

16s_bayes_co-occurrence

for 16S bayesian co-occurrence project

16snetworks

2021_dvrfs_microbiome

Scripts for a manuscript titled "Subsurface Planktonic Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity" (submitted)

acnc-dame

Dynamic Assessment of Microbial Ecology

amplicon

Statistics and visualization for amplicon data

amplicon2017

Data and scripts for amplicon pipeline

ampliconnetwork_deserts

ankspon

Files for recapitulating microbiome analysis

banocc

BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`

bio381

bioinformatics

试试在这里放一些生物信息的东西，并且学会使用

blogofxiaoming

小明的数据分析笔记本 推文合集

bpd_rest

Graph analyses of BPD rest data

co-occurrence

R scripts for performing co-occurrence analyses

co-occurrence_networks

Scripts for null model analysis of plant-mycorrhiza co-occurrence networks described in Encinas-Viso et al (2016)

codyn

:exclamation: This is a read-only mirror of the CRAN R package repository. codyn — Community Dynamics Metrics. Homepage: https://github.com/NCEAS/codyn/ Report bugs for this package: https://github.com/NCEAS/codyn/issues

comma

Community Matrix Analysis

community_assembly

consistent-effects-of-independent-domestication-events-on-seed-microbiome

cooc_compare

Supplementary code for co-occurrence analyses of Barner et al. (2018, Ecology) Appendices S1 and S2

cooccur

Probabilistic Species Co-occurrence Analysis in R

crc-udca2

Analyses for UDCA Cancer Research submission

dawg2019

Fungal ITS pyrosequencing data provided by Dr. Bert Eardley

doing-bayesian-data-analysis-in-brms-and-the-tidyverse

The bookdown version lives here: https://bookdown.org/content/3686

doodads

These are those littlebits of code and tutorials that someone else wrote and I used/modified. I imagine people who work in my lab and department will find some of these useful. I try to give credit via links in the script, please let me know if I left you out. I'm not trying to take credit for anyone else's work! Some of these gems might be my own work.

easy_microbiome

R 16S

easyamplicon

Easy Amplicon data analysis pipeline

easynetwork

R scripts to construct co-occurrence network

ecological-sems-in-lavaan

Recreating SEM analyses from papers using the R lavaan package