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aws-doc-sdk-examples

Welcome to the AWS Code Examples Repository. This repo contains code examples used in the AWS documentation, AWS SDK Developer Guides, and more. For more information, see the Readme.md file below.

aws-for-bioinformatics

AWS for Bioinformatics Researchers

aws-genomics-nextflow-workshop

aws-genomics-workflows

Genomics Workflows on AWS

aws-sagemaker

aws-step-functions-lambda-python

bactopia

A flexible pipeline for complete analysis of bacterial genomes

bam-filter

A simple tool to calculate metrics from a BAM file and filter references with uneven coverages

bam-readcount

count DNA sequence reads in BAM files

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

bamsifter

normalizes coverage depth by position-specific read sampling in a bam file to give a target max depth

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

bash-it

A community Bash framework.

basics

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

bat

BAT - Bisulfite Analyss Toolkit

bayesian-analysis-recipes

A collection of Bayesian data analysis recipes using PyMC3

bayesian-stats-talk

Doing Bayesian statistics in Python!

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bcool

de Bruijn graph cOrrectiOn from graph aLignment

bdqc

Big Data Quality Control

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

beacontoolkit

Tools for working with modern scientific data

bedtools

A powerful toolset for genome arithmetic.

bedtools-protocols

bedtools2

A powerful toolset for genome arithmetic.

benchm-ml

A minimal benchmark for scalability, speed and accuracy of commonly used open source implementations (R packages, Python scikit-learn, H2O, xgboost, Spark MLlib etc.) of the top machine learning algorithms for binary classification (random forests, gradient boosted trees, deep neural networks etc.).

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

biancur-cellmetabolism-2020

Corresponding code and figures for publication of Biancur DE, Kapner KS, Yamamoto K, Banh RS, Neggers JE, Sohn ASW, Wu W, Manguso R, Brown A, Root D, Aguirre AJ, Kimmelman AC. Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer. Cell Metabolism, 2020, In Press.