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anndata

Annotated data.

basic_flask_template

Simple flask server for display static image results

cellassign-1

Automated, probabilistic assignment of cell types in scRNA-seq data

cellassign-tool

Container for running cellassign.

clonealign

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

clonealign-tool

Container for running clonealign.

cri_bioinformatics_workshop

Tutorials and code for CRI bioinformatics workshop.

fastmi

Rust binding for mutual information calculation.

genevector

Vector representations of gene co-expression in single cell RNAseq.

genevector-documentation

GeneVector Documentation and Tutorials

grafiti

Grafiti

grimoire

Magical spells for simple scRNA tasks.

gseapynet

Running GSEA with network view of pathways.

hebbian

Boolean Hebbian learning framework

honeybadger

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

howstheweath

Random Forests - Model Comparison(SKlearn)

language-exercises

Language exercises from "Exercises in Programming Languages" - Cristina Lopes

mudata

Multimodal Data (.h5mu) implementation for Python

muon

muon is a multimodal omics Python framework

nceglia.github.io

Nick's blog

nickypl

Custom Compiler - CFG & DOM -> CSE, Copy Propagation, IR, compiles with nasm

pycurve

pypeliner

rnascp

Pure rust singe cell rnaseq pseudo alignment pipeline.

rnasecondarystructure

Genetic Algortihm

rust-debruijn

De Bruijn graphs in Rust

rust-exercism

Using Rust to solve exercises

rust-pseudoaligner

Single-Cell RNA-seq pseudo-aligner

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.