Pinned Repositories
2018-10-09-embl
academic_website
atom-language-julia
A Julia language support package for the Atom editor
BEAR
A Better Sequencing Simulator for Metagenomics
LatentStrainAnalysis
Partitioning and analysis methods for large, complex sequence datasets
SLIC
Web app to design primers for SLIC.
sysbio
Webpage for the SysBio retreat
latent-lego
Latent spaces for single cells
Pando
Multiome GRN inference.
VoxHunt
VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
joschif's Repositories
joschif/LatentStrainAnalysis
Partitioning and analysis methods for large, complex sequence datasets
joschif/sysbio
Webpage for the SysBio retreat
joschif/2018-10-09-embl
joschif/academic_website
joschif/atom-language-julia
A Julia language support package for the Atom editor
joschif/BEAR
A Better Sequencing Simulator for Metagenomics
joschif/SLIC
Web app to design primers for SLIC.
joschif/CONCOCT
Clustering cONtigs with COverage and ComposiTion
joschif/DElegate_covar
Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
joschif/ENA-downloader
Downloads read files from ENA.
joschif/glulight
Glucose lamp
joschif/instabot
Artistic af, man! 🔥
joschif/jupytext
Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts
joschif/LSHash
A fast Python implementation of locality sensitive hashing.
joschif/markdown-cv
a simple template to write your CV in a readable markdown file and use CSS to publish/print it.
joschif/merlot
Reconstruct the lineage topology of a scRNA-seq differentiation dataset.
joschif/mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
joschif/mOTUs_v2
motus - a tool for marker gene-based OTU (mOTU) profiling
joschif/Pando
Multiome GRN inference.
joschif/plotting
Some scripts for plotting
joschif/pystruct
Simple structured learning framework for python
joschif/rstudio_atom_theme
Contains a CSS file that styles a selected RStudio editor theme the atom way
joschif/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
joschif/scripts
Collection of more or less helpful little scripts.
joschif/scvi-tools
Deep probabilistic analysis of single-cell omics data
joschif/seqlearn
Sequence learning toolkit for Python
joschif/signac
R toolkit for the analysis of single-cell chromatin data
joschif/slingshot
Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
joschif/VoxHunt
VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
joschif/website