dawe

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

Circe

Co-accessibility network from ATAC-seq data. Python code, based on Cicero package (R).

figeno

Tool for plotting sequencing data along genomic coordinates.

matmulfreellm

Implementation for MatMul-free LM.

stumpy

STUMPY is a powerful and scalable Python library for modern time series analysis

gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

pykan

Kolmogorov Arnold Networks

hypergraphx

HGX is a multi-purpose, open-source Python library for higher-order network analysis

openproblems-v2

Formalizing and benchmarking open problems in single-cell genomics

ComplexNetworks2021-tda-crash-courses

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

llms_from_dummies

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

risultati-asn

Elenco quotidiano dei risultati ASN

milopy

Python implementation of Milo for differential abundance testing on KNN graph

CONGASp

rcongas

rcongas

congas

A set of Pyro models and functions to infer CNA from scRNA-seq data

sparsecca

Python implementations for Sparse CCA

learning

materials for learing various stuff by doing them myself

xbgzip

Fast streams for block gzip files.

Laplacian-RG

Laplacian Renormalization Group for heterogeneous networks

codon

A high-performance, zero-overhead, extensible Python compiler using LLVM

schist

An interface for Nested Stochastic Block Model for single cell analysis

cfDNA

cfDNA analysis workflow

core-periphery-detection

Python package for detecting core-periphery structure in networks.

SurpriseMeMore

Module to detect mesoscale structures (community, core-periphery, bipartite) on Graphs and Multigraphs using surprise.

infomap

Multi-level network clustering based on the Map Equation

NEMtropy

A python3 module for maximum entropy models on networks.