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awesome

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

awesome-1

:sunglasses: Curated list of awesome lists

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-flask

A curated list of awesome Flask resources and plugins

bam2x

extract information from bam (sequence alignment) files and generate tables for further analysis.

bayesboost

Bayesian Optimization using xgboost and sklearn API

bayesianoptimization

A Python implementation of global optimization with gaussian processes.

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

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.).

bic-rnaseq

Bioinformatics core RNAseq pipeline

bic-variants_pipeline

BIC@MSKCC Variants Pipeline

bokeh

Interactive Web Plotting for Python

bootstrap

The most popular HTML, CSS, and JavaScript framework for developing responsive, mobile first projects on the web.

bwa-meth

fast and accurate alignment of BS-Seq reads

cfdnapattern

Pattern Recognition for Cell-free DNA

cheatsheets

Quick lookup documents for commonly used tools

checkmyindex

Search for a set of compatible indexes for your sequencing experiment

cnvkit

Copy number variant detection from targeted DNA sequencing

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

complexheatmap

make complex heatmaps as well as self define annotation graphics

ctcnv

A new CNV calling method for DNA-seq data

cyrest

RESTful API Module for Cytoscape 3.2.1+

cyvcf

A fast Python library for VCF files leveraging Cython for speed.

cyvcf2

cython + htslib == fast VCF parsing

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

delfi_scripts

dplython

dplyr for python

duplex-sequencing

enrichr

A hacky little interface to call the Enrichr functional enrichment tool from R.