pwl

ripgrep

ripgrep recursively searches directories for a regex pattern while respecting your gitignore

umap

Uniform Manifold Approximation and Projection

ArchWSL

ArchLinux based WSL Distribution. Supports multiple install.

deepo

Setup and customize deep learning environment in seconds.

python3_with_pleasure

A short guide on features of Python 3 with examples

DifferentialEquations.jl

Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components. Ordinary differential equations (ODEs), stochastic differential equations (SDEs), delay differential equations (DDEs), differential-algebraic equations (DAEs), and more in Julia.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

fieldplay

A vector field explorer

mcmc-demo

Interactive Markov-chain Monte Carlo Javascript demos

ffjord

code for "FFJORD: Free-form Continuous Dynamics for Scalable Reversible Generative Models".

bravado

Bravado is a python client library for Swagger 2.0 services

magnet

Deep Learning Projects that Build Themselves

noise2self

A framework for blind denoising with self-supervision.

emacs-python-pytest

run pytest inside emacs

dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

networkanalysis

Java package that provides data structures and algorithms for network analysis.

UMAP.jl

Uniform Manifold Approximation and Projection (UMAP) implementation in Julia

clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

TopicModelsVB.jl

A Julia package for variational Bayesian topic modeling.

scvae

Deep learning for single-cell transcript counts

UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

scone

SpectralClustering.jl

Spectral clustering algorithms written in Julia

org-re-reveal

Org export to reveal.js presentations

BayesFlow

GrandPrix

GrandPrix

matrix-service

DCP Expression Matrix Service

iv.opv.package

Scripts used in my PhD project