schelhorn

depiction

interpret deep learning models in a framework-independent fashion

fst

Lightning Fast Serialization of Data Frames for R

composer

Visual and code editor for Common Workflow Language

bunny

[Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0

protect

restic

Fast, secure, efficient backup program

kallisto

Near-optimal RNA-Seq quantification

readr

Read flat files (csv, tsv, fwf) into R

arvados

An open source platform for managing and analyzing biomedical big data

hail

Cloud-native genomic dataframes and batch computing

og-aws

📙 Amazon Web Services — a practical guide

awesome-selfhosted

A list of Free Software network services and web applications which can be hosted on your own servers

deeplearning-biology

A list of deep learning implementations in biology

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

image-analogies

Generate image analogies using neural matching and blending.

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

bcbio-nextgen-monitor

Monitor the status of bcbio-nextgen analyses

OpenSensorsPythonTools

leaflet

R Interface to Leaflet Maps

dna-traits

A fast 23andMe genome text file parser, now superseded by arv

readxl

Read excel files (.xls and .xlsx) into R 🖇

referee

ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

hisat2

Graph-based alignment (Hierarchical Graph FM index)

cnvkit

Copy number variant detection from targeted DNA sequencing

miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

twitrssme

TwitRSS.me: Tool to make Twittter timelines and searches into RSS feeds