xxz19900

16srDNA_analysis_system

16SrRNA-hex-tutorial

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

awesome-tensorflow

TensorFlow - A curated list of dedicated resources http://tensorflow.org

ML-From-Scratch

Machine Learning From Scratch. Bare bones Python implementations of Machine Learning models and algorithms with a focus on transparency and accessibility. Aims to cover everything from Data Mining to Deep Learning.

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pydata-notebook

利用Python进行数据分析 第二版 (2017) 中文翻译笔记

Sniffles

Structural variation caller using third generation sequencing

amplicon_sequencing_pipeline

Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.

Basecalling-comparison

A comparison of different Oxford Nanopore basecallers

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

data.table

R's data.table package extends data.frame:

GenomicConsensus

PacBio® variant and consensus caller

hominid

Hominid: host-microbiome interaction identification

In-depth-NGS-Data-Analysis-Course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

MICB405-Metagenomics

A metagenome annotation workflow for UBC's Microbiology 405 course, Bioinformatics

MicrobialGenomeMetagenomeCourse

Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017

microbiomeGWAS

microbiomeHD

Cross-disease comparison of case-control gut microbiome studies

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

NA12878

Data and analysis for NA12878 genome on nanopore

ordination101

Ordination lectures for Ecological Methods in Oulu

qiime

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

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116

rigraph

igraph R package

Schloss_PacBio16S_PeerJ_2015

Repository to accompany "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system"

STAT545-UBC.github.io

Main repository for STAT 545 @ University of British Columbia, a course in data wrangling, exploration, and analysis with R.

Tensorflow-101

TensorFlow Tutorials

Tools-Microbiome-Anlaysis

A list of R environment based tools for marker gene microbiome data exploration, statistical analysis and visualization