vreuter
Computational biology software, with interest in analyzing genome architecture and regulation by imaging and sequencing.
Pinned Repositories
pypiper
Python toolkit for building restartable pipelines
looper
A job submitter for Portable Encapsulated Projects
peppy
Project metadata manager for PEPs in Python
refgenie
Reference genome resource manager
adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
aicspylibczi
Python module utilizing libCZI for reading Zeiss CZI files.
haskell-exercises-ThinkingFunctionally-RichardBird
Haskell exercises, Thinking Functionally with Haskell by Richard Bird
peppy
A python-based project metadata manager for portable encapsulated projects
python-type-stubs
A set of type stubs for popular Python packages. These are works in progress from the Microsoft Python team and others, with the intent that they are contributed to typeshed or to the associated packages once sufficiently complete.
vreuter's Repositories
vreuter/bedtools2
A powerful toolset for genome arithmetic.
vreuter/bwtool
A tool for bigWig files.
vreuter/changepoint
A place for the development version of the changepoint package on CRAN.
vreuter/clusterProfiler
:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters
vreuter/contrastive
Contrastive PCA
vreuter/deepTools
Tools to process and analyze deep sequencing data.
vreuter/GeneSets
A set of scripts to build gene set databases for use with the SetRank gene set enrichment analysis package.
vreuter/haskell-exercises
Haskell exercises with automatic tests
vreuter/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
vreuter/hydeout
A refreshed version of Hyde for Jekyll 3.x
vreuter/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
vreuter/latex_interactive_slides
Demo for combining beamer, tikz, and hyperref to create an interactive slide show
vreuter/learn-you-a-haskell-exercises
vreuter/logme
Python Logging For Humans (Also supports configurable color logging for the terminal!)
vreuter/math-as-code
a cheat-sheet for mathematical notation in code form
vreuter/msigdbr
MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
vreuter/omictools
Genomics and epigenomics types and tools, in Scala
vreuter/open_pipelines
vreuter/openvax-project-template
Template for a new OpenVax Python project
vreuter/os-lib
OS-Lib is a simple Scala interface to common OS filesystem and subprocess APIs
vreuter/pepr
vreuter/pilon
Pilon is an automated genome assembly improvement and variant detection tool
vreuter/plastid
Position-wise analysis of sequencing and genomics data
vreuter/recursion-schemes-lc2018
Rrecursion schemes without the barbed wire
vreuter/rigraph
igraph R package
vreuter/scala
The Scala programming language
vreuter/scopt
simple scala command line options parsing
vreuter/SetRank
An R package for advanced gene set enrichment analysis on the results of genomics experiments.
vreuter/SetRank_interactomes
A set of scripts to build interactome objects for use with the SetRank package.
vreuter/TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models