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anndata

Annotated data matrix.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bbknn

Batch balanced KNN

cdpc

cellrank

CellRank for directed single-cell fate mapping

dawe.github.io

Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

discan

dsptool

A general DSP tool for processing genomic data

ecosystem-packages

Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

fit_nbinom

Negative binomial maximum likelihood estimate implementation in Python using L-BFGS-B

hicexplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

kallisto

Near-optimal RNA-Seq quantification

mofa

Multi-Omics Factor Analysis

mofapy2

Multi-omics factor analysis v2

sbmcommunitydetection

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scatacc

Things needed for custom scATAC analysis

scget

schist

An interface for Nested Stochastic Block Model for single cell analysis

schist-feedstock

A conda-smithy repository for schist.

schist-notebooks

Some example notebooks for scNSBM package

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

scikit-fusion

scikit-fusion: Data fusion via collective latent factor models

sctips_twitter

Some random code about single cell stuff to share with my Tweeps

sinto

Tools for single-cell data processing

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

surprisememore

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

tensorly

TensorLy: Tensor Learning in Python.

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets