Silas Kieser's repositories
YAMP
YAMP: Yet Another Metagenomic Pipeline
scopus
Python API for Accessing Scopus databases with their REST API
picrust
Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests
scholar.py
A parser for Google Scholar, written in Python
metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
article-downloader
Uses publisher APIs to programmatically retrieve large amounts of scientific journal articles for text mining.
LatentStrainAnalysis
Partitioning and analysis methods for large, complex sequence datasets
openface
Face recognition with deep neural networks.
megahit
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
blog-assets
Source codes for some posts on my blogs.
try-tf
Simple code for trying out TensorFlow with simulated datasets
plotly.py
the browser-based graphing library for python
networkx
Official NetworkX source code repository.
statsintro
Introduction to Statistics
scLVM
scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
Theano
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.
snakemake-workflows
An experimental repo for common snakemake rules and workflows
statsmodels
Statsmodels: statistical modeling and econometrics in Python
ipython
Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.
bbcfutils
Collection of stand-alone tools
d3
A JavaScript visualization library for HTML and SVG.
impress.js
It's a presentation framework based on the power of CSS3 transforms and transitions in modern browsers and inspired by the idea behind prezi.com.
epfl-moodle
Sane interface to moodle
bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
cruzdb
python access to UCSC genomes database
scipy2014_tutorial
Tutorial: Bayesian Statistical Analysis in Python
pymc-examples
PyMC Example Notebooks
hmm
Hidden Markov Models in various languages