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pathogen-identification

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

phyloseq-extended

Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul

phyloseq_translate

phyloseq R

pig-colonization-history-study

pigargs

Codes related to the manuscript "Characteristics and host bacteria of resistome in pigs raised in farms with different management patterns".

pigc

The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.

probability

Probabilistic reasoning and statistical analysis in TensorFlow

python-ecology-lesson

Data Analysis and Visualization in Python for Ecologists

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

qiime-2-based-16s-analysis

r-novice-gapminder

Introduction to R for non-programmers using gapminder data.

r-workshops

R workshop slides and information

reinforcement-learning

Implementation of Reinforcement Learning Algorithms. Python, OpenAI Gym, Tensorflow. Exercises and Solutions to accompany Sutton's Book and David Silver's course.

rgcookbook

R Graphics Cookbook

rna-seq-analysis

RNAseq analysis notes from Ming Tang

r_for_biologists

Scripts and data for Plotting in R for Biologists, a video course on YouTube

sadams23.github.io

seqtk

Toolkit for processing sequences in FASTA/Q formats

sradb_tools

talkguide

The Leek Group Guide to Giving Talks

target-enrichment-of-metazoan-mitochondrial-dna-with-hybridization-capture-probes

code and tutorials for data analyses related to the manuscript submitted to Ecological Indicators

taxonomic-abundance-mapping

Taxonomy Abundance Profiling of Metagenomic Reads

tcgasurvival

Scripts to analyze TCGA data

teaching_2018

the_interactome

This repository is a part of a publication that has been recently accepted for publication at Nature Medicine.

tong-s_must_read_list

papers read list about biology, bioinformatics, and others

whirlwindtourofpython

The Jupyter Notebooks behind my OReilly report, "A Whirlwind Tour of Python"

zhang2019nbt

Scripts for stat and plot figures in rice microbiome paper