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giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

glue_pc

GLUE_PC: Global Urban Evolution Project — Parallel Clines

google-access-helper

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gpd

This repository contains scripts used in the manuscript "Massive expansion of human gut bacteriophage diversity"

gunc

Python package for detection of chimerism and contamination in prokaryotic genomes.

humann

HUMAnN 2.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

intro-to-chipseq

Intro to ChIPseq using HPC

kraken2

The second version of the Kraken taxonomic sequence classification system

machine-learning

Machine learning and Me learning

mashtree

:deciduous_tree: Create a tree using Mash distances

metachip

Horizontal gene transfer (HGT) identification pipeline

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

metgenomics_pilot

mgs-gut

Analysing Metagenomic Species (MGS)

microbiomestatplot

Interpretation and visualization of microbiome charts

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

moby

Moby Project - a collaborative project for the container ecosystem to assemble container-based systems

neptuneyt.github.io

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

nobug

Paradigm for no bug in your code forever

non-model_function_enrichment_tools

Some bioinformic domestic scripts.

novel-species-identifier

Novel species identifier - METAnnotatorX custom-made script

parallel-meta

A High Performance Microbiome Analysis Toolkit.

phagehosts

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

phageparser

A project to extract CRISPR information from open genetic data.

phamers

A bioinformatic tool for identifying bacteriophages using machine learning and k-mers

phyloflash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

picturedatabases

playground

programmatic games, just for fun

pycorrector

pycorrector is a toolkit for text error correction. 文本纠错，Kenlm，ConvSeq2Seq，BERT，MacBERT，ELECTRA，ERNIE，Transformer，T5等模型实现，开箱即用。