jonas's repositories
LatentStrainAnalysis
Partitioning and analysis methods for large, complex sequence datasets
atom-language-julia
A Julia language support package for the Atom editor
BEAR
A Better Sequencing Simulator for Metagenomics
SLIC
Web app to design primers for SLIC.
CONCOCT
Clustering cONtigs with COverage and ComposiTion
DElegate_covar
Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
ENA-downloader
Downloads read files from ENA.
glulight
Glucose lamp
instabot
Artistic af, man! 🔥
jupytext
Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts
LSHash
A fast Python implementation of locality sensitive hashing.
markdown-cv
a simple template to write your CV in a readable markdown file and use CSS to publish/print it.
merlot
Reconstruct the lineage topology of a scRNA-seq differentiation dataset.
mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
mOTUs_v2
motus - a tool for marker gene-based OTU (mOTU) profiling
Pando
Multiome GRN inference.
plotting
Some scripts for plotting
pystruct
Simple structured learning framework for python
rstudio_atom_theme
Contains a CSS file that styles a selected RStudio editor theme the atom way
scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
scripts
Collection of more or less helpful little scripts.
scvi-tools
Deep probabilistic analysis of single-cell omics data
seqlearn
Sequence learning toolkit for Python
signac
R toolkit for the analysis of single-cell chromatin data
slingshot
Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
VoxHunt
VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps