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16srrna-hex-tutorial

16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.

2017_metasnv

Repository containing metaSNV codes

bioinformatics-algorithms

Algorithms for bioniformatics analysis. Examples include randomized motif search, Baum-Welch learning, Viterbi learning, Soft Decoding, and DAG algorithm

blca

c-log

a fast ,stable and thread-safe log lib(logger) for C/C++ language

clonalorigin

Inference of homologous recombination in bacteria using whole genome sequences

clusterphlan

Pipeline of metaphlan2 and strainphlan for the cluster with Grid Engine

designers-learn-git

为设计师而作的GitHub的快速学习教程

flash

Unofficial repo for software vendoring or packaging purposes

flash2

Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons

flexbar

flexible barcode and adapter removal

flexbar-1

Unofficial repo for software vendoring or packaging purposes

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

irfinder

Detecting intron retention from RNA-Seq experiments

lexsimulator

Lex词法分析器模拟器

lihang

Statistical learning methods, 统计学习方法(第2版)[李航] [笔记, 代码, notebook, 参考文献, Errata, lihang]

lihang_book_algorithm

致力于将李航博士《统计学习方法》一书中所有算法实现一遍

machinelearning

My blogs and code for machine learning. http://cnblogs.com/pinard

machinelearningalgorithm

Implementation of some machine learning algorithms

machinelearninginaction

Source Code for the book: Machine Learning in Action published by Manning

metasnv

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

mlst

:id: Scan contig files against PubMLST typing schemes

nn-svg

Publication-ready NN-architecture schematics.

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

python-rosalind

This repository contains my Rosalind answers for all of the following questions (all have been tested and work): Installing Python Counting DNA Nucleotides Strings and Lists Working with Files Dictionaries Transcribing DNA into RNA Translating RNA into Protein Find the Reverse Complement of a String Inferring mRNA from Protein Transitions and Transversions Generate the k-mer Composition of a String Reconstruct a String from its Genome Path Constructing a De Bruijn Graph Open Reading Frames Counting Point Mutations Finding a Motif in DNA Edit Distance Edit Distance Alignment Finding a Shared Motif Creating a Distance Matrix Construct the Suffix Array of a String Reconstruct a String from its Burrows-Wheeler Transform Enumerating Gene Orders Enumerating Oriented Gene Orderings RNA Splicing Finding a Spliced Motif Mendel's First Law Compute the Probability of a Hidden Path Compute the Probability of an Outcome Given a Hidden Path Implement the Viterbi Algorithm Conditions and Loops Mortal Fibonacci Rabbits Finding a Protein Motif Error Correction in Reads Global Alignment with Scoring Matrix Local Alignment with Scoring Matrix

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.