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particlefilter

Particle filtering inference for stochastic dynamical systems

phantompy

Python analog of the PhantomPurgeR algorithm to remove index-swapped reads in RNAseq

pybustools

Python functions to read the kallisto-bustools format

pydiffusionmaps

Diffusion maps for python

pyhematofateprediction

Python code to [Buggenthin2017]

pynndescent

A Python nearest neighbor descent for approximate nearest neighbors

pytidyverse

Convenience for importing standard packages

rc2015

Reading Course 2015: Quantitative stem cell biology

redst4r.github.io

riemannian_latent_space

Riemannian metrics to measure distances in latent space of VAEs

rnaseqtools

Python code for handling various aspects of RNAseq data

rust_shadow

rnaseq error estimation in rust

rustbustools

Kallisto bustools in Rust

rustphantompurger

Rust implementation of PhantomPurger

scanpy

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

sccoda

A statistical test for compositional changes in scRNA

schclpy

A simplistic python version of the scHCL R package

scpysingscore

Like singscore, but for single cell rna-seq. Made for scanpy anndata objects.

scrnaseq_cb_reveal

scsim

Simulate single-cell RNA-SEQ data using the Splatter statistical framework but implemented in python. In addition, simulate doublet cells and cells with shared gene-expression programs.

scsnp

SNP detection in single cell sequencing data

sctools

Tools that come handy when working in scanpy all day long

seclists

SecLists is the security tester's companion. It's a collection of multiple types of lists used during security assessments, collected in one place. List types include usernames, passwords, URLs, sensitive data patterns, fuzzing payloads, web shells, and many more.

souporcell

Clustering scRNAseq by genotypes

spearmint

Spearmint Bayesian optimization codebase

stacked_denoising_autoencoders

trying to redo the Vincent2010 paper

tree-inference

unifracpy

Python implementation of the uniFrac distance measure

unseenspecies

Unseen species estimators