Pinned Repositories
atlas
ATLAS - Three commands to start analyzing your metagenome data
16S-dada2
Snakemake pipeline for amplicon sequencing using dada2
Bubbleplot
FastDrep
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
ipath3
Python wrapper for ipath3
Krak
Snakemake for flexitaxd and Kraken2
stamps2019
Materials for the STAMPS 2019 course at the MBL in Woods Hole, MA, USA
statsplot
SilasK's Repositories
SilasK/article-downloader
Uses publisher APIs to programmatically retrieve large amounts of scientific journal articles for text mining.
SilasK/bbcfutils
Collection of stand-alone tools
SilasK/bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
SilasK/blog-assets
Source codes for some posts on my blogs.
SilasK/d3
A JavaScript visualization library for HTML and SVG.
SilasK/d3-collapsible-tree-demo
Example of displaying data in a collapsible tree using D3.js
SilasK/deepdream
SilasK/epfl-moodle
Sane interface to moodle
SilasK/evolving-simple-organisms
Evolving simple organisms using a genetic algorithm and deep learning from scratch with python
SilasK/hugo-agency-theme
Port of Startbootstrap's Agency theme to Hugo
SilasK/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.
SilasK/ipython
Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.
SilasK/LatentStrainAnalysis
Partitioning and analysis methods for large, complex sequence datasets
SilasK/megahit
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
SilasK/metagenomics-workshop
Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm
SilasK/networkx
Official NetworkX source code repository.
SilasK/openface
Face recognition with deep neural networks.
SilasK/picrust
Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests
SilasK/plotly.py
the browser-based graphing library for python
SilasK/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 ;)
SilasK/scholar.py
A parser for Google Scholar, written in Python
SilasK/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.
SilasK/scopus
Python API for Accessing Scopus databases with their REST API
SilasK/slurm
Cookiecutter for snakemake slurm profile
SilasK/snakemake-workflows
An experimental repo for common snakemake rules and workflows
SilasK/statsintro
Introduction to Statistics
SilasK/statsmodels
Statsmodels: statistical modeling and econometrics in Python
SilasK/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.
SilasK/try-tf
Simple code for trying out TensorFlow with simulated datasets
SilasK/YAMP
YAMP: Yet Another Metagenomic Pipeline