egekcmz's repositories
ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
sra-tools
SRA Tools
C-WAP
SC2 variant detection and composition pipeline
spark-moderndataengineering
The source code for the book Modern Data Engineering with Apache Spark
augur
Pipeline components for real-time phylodynamic analysis
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
bioconda-recipes
Conda recipes for the bioconda channel.
aws-cli
Universal Command Line Interface for Amazon Web Services
pip
The Python package installer
opencv
Open Source Computer Vision Library
cli
The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.
auspice
Web app for visualizing pathogen evolution
dbvar
dbVar
psutil
Cross-platform lib for process and system monitoring in Python
faunadb-python
Python driver for FaunaDB
VaQuERo
SARS-CoV-2 (Va)riant (Qu)antification in s(E)wage, designed for (Ro)bustness
hisat2
Graph-based alignment (Hierarchical Graph FM index)
rethinkdb
The open-source database for the realtime web.
cvxopt
CVXOPT -- Python Software for Convex Optimization
DeViVa
Scripts for analyzing SARS-CoV-2 variants
datrie
Fast, efficiently stored Trie for Python. Uses libdatrie.
IQ-TREE
Efficient phylogenomic software by maximum likelihood
Bioinformatics-with-Python-Cookbook-Second-Edition
Bioinformatics with Python Cookbook Second Edition, published by Packt
vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.