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100daysofcode

PyBites #100DaysOfCode

2015

Public material for CS109

adafruit-pi-finder

Find and set up your brand new Raspberry Pi

aimhii

arkin

Tools and scripts from the Arkin Lab at UC Berkeley

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

assembly

Pipelines for assembling NGS data from Seattle flu study.

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

ballgown

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

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

beautiful_idiomatic_python

Notes from Raymond Hettinger's talk at PyCon US 2013.

binning

Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85

biocode

Bioinformatics code libraries and scripts

biocompoundml

BioCompoundML is a software tool for rapidly screening chemicals by chemical properties, using machine learning.

biodock

A Docker container that runs bioinformatics software.

bioinformatics-programming-using-python

Exercises from the 'Bioinformatics Programming using Python' book by Mitchell L Model

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

bremdata

bulkvis

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

canu

A single molecule sequence assembler for genomes large and small.

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

challenges

PyBites Code Challenges

code

ActiveState Code Recipes

comparative-annotation-toolkit

concoct

Clustering cONtigs with COverage and ComposiTion

courses

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