satopan

metamicrobiomeR

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models

googlyPlusPlus

Emmys-NoteBooks

Random notebooks for various projects.

locatr

An easier way to tidying pivoted tables.

RVA

RNAseq Visualization Automation

mlreview_notebooks

Jupyter notebooks for "A high-bias, low-variance introduction to Machine Learning for physicists"

TokyoCovidMonitor

An R package for monitoring the trend of daily COVID-19 positive cases in Tokyo

humann

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

MedicalAI-UAP

BiomeNED

BiomeNED main code

Bioinformatics-with-Python-Cookbook-Second-Edition

Bioinformatics with Python Cookbook Second Edition, published by Packt

R-Bioinformatics-Cookbook

R Bioinformatics Cookbook, published by Packt

LearningWith_BioinformaticsWithPythonCookbook_2nd

Learning note of "Bioinformatics with Python Cookbook - Second Edition"

AGPMicrobiomeHostPredictions

A broad search for significant microbiome-modifying host variables from the American Gut Project public microbiome data

network-analysis-in-biology

「生物ネットワーク解析」の補足資料

cy-rest-R

Example R script to use Cytoscape via RESTful API module.

md2googleslides

Generate Google Slides from markdown

AHMbook

R package with functions and data for the book 'Applied Hierarchical Modeling in Ecology'

AHM_code

Code from the book 'Applied Hierarchical Modeling in Ecology'

MK-SpikeSeq

Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples

microbiome-assembly

Code associated with "Ecological rules for the assembly of microbiome communities"

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

GMPR

Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data

corncob

Count Regression for Correlated Observations with the Beta-binomial

jpaRmd

ConfusionTableR

a package to collapse the outputs of CARET's confusion matrix for storage in database tables

targets-shiny

Example Shiny app containing a targets pipeline.

tidyMicro

tidyMicro GitHup Repository

r-sparcc

R package computes correlation for relative abundances