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

Overview

Stars PyPI PyPIDownloads BiocondaDownloads Docs Build Status

Scanpy – Single-Cell Analysis in Python

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Discuss usage on Discourse. Read the documentation. If you'd like to contribute by opening an issue or creating a pull request, please take a look at our contributing guide. If Scanpy is useful for your research, consider citing Genome Biology (2018).

Owner
Theis Lab
Institute of Computational Biology
Theis Lab
Transform-Invariant Non-Negative Matrix Factorization

Transform-Invariant Non-Negative Matrix Factorization A comprehensive Python package for Non-Negative Matrix Factorization (NMF) with a focus on learn

EMD Group 6 Jul 01, 2022
Python implementation of Principal Component Analysis

Principal Component Analysis Principal Component Analysis (PCA) is a dimension-reduction algorithm. The idea is to use the singular value decompositio

Ignacio Darago 1 Nov 06, 2021
The official repository for ROOT: analyzing, storing and visualizing big data, scientifically

About The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficien

ROOT 2k Dec 29, 2022
WithPipe is a simple utility for functional piping in Python.

A utility for functional piping in Python that allows you to access any function in any scope as a partial.

Michael Milton 1 Oct 26, 2021
Deep universal probabilistic programming with Python and PyTorch

Getting Started | Documentation | Community | Contributing Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. Notab

7.7k Dec 30, 2022
This is a python script to navigate and extract the FSD50K dataset

FSD50K navigator This is a script I use to navigate the sound dataset from FSK50K.

sweemeng 2 Nov 23, 2021
Full ELT process on GCP environment.

Rent Houses Germany - GCP Pipeline Project: The goal of the project is to extract data about house rentals in Germany, store, process and analyze it u

Felipe Demenech Vasconcelos 2 Jan 20, 2022
Wafer Fault Detection - Wafer circleci with python

Wafer Fault Detection Problem Statement: Wafer (In electronics), also called a slice or substrate, is a thin slice of semiconductor, such as a crystal

Avnish Yadav 14 Nov 21, 2022
A pipeline that creates consensus sequences from a Nanopore reads. I

A pipeline that creates consensus sequences from a Nanopore reads. It clusters reads that are similar to each other and creates a consensus that is then identified using BLAST.

Ada Madejska 2 May 15, 2022
fds is a tool for Data Scientists made by DAGsHub to version control data and code at once.

Fast Data Science, AKA fds, is a CLI for Data Scientists to version control data and code at once, by conveniently wrapping git and dvc

DAGsHub 359 Dec 22, 2022
CINECA molecular dynamics tutorial set

High Performance Molecular Dynamics Logging into CINECA's computer systems To logon to the M100 system use the following command from an SSH client ss

J. W. Dell 0 Mar 13, 2022
X-news - Pipeline data use scrapy, kafka, spark streaming, spark ML and elasticsearch, Kibana

X-news - Pipeline data use scrapy, kafka, spark streaming, spark ML and elasticsearch, Kibana

Nguyễn Quang Huy 5 Sep 28, 2022
Automated Exploration Data Analysis on a financial dataset

Automated EDA on financial dataset Just a simple way to get automated Exploration Data Analysis from financial dataset (OHLCV) using Streamlit and ta.

Darío López Padial 28 Nov 27, 2022
Reading streams of Twitter data, save them to Kafka, then process with Kafka Stream API and Spark Streaming

Using Streaming Twitter Data with Kafka and Spark Reading streams of Twitter data, publishing them to Kafka topic, process message using Kafka Stream

Rustam Zokirov 1 Dec 06, 2021
Snakemake workflow for converting FASTQ files to self-contained CRAM files with maximum lossless compression.

Snakemake workflow: name A Snakemake workflow for description Usage The usage of this workflow is described in the Snakemake Workflow Catalog. If

Algorithms for reproducible bioinformatics (Koesterlab) 1 Dec 16, 2021
Data and code accompanying the paper Politics and Virality in the Time of Twitter

Politics and Virality in the Time of Twitter Data and code accompanying the paper Politics and Virality in the Time of Twitter. In specific: the code

Cardiff NLP 3 Jul 02, 2022
Scraping and analysis of leetcode-compensations page.

Leetcode compensations report Scraping and analysis of leetcode-compensations page.

utsav 96 Jan 01, 2023
PySpark bindings for H3, a hierarchical hexagonal geospatial indexing system

h3-pyspark: Uber's H3 Hexagonal Hierarchical Geospatial Indexing System in PySpark PySpark bindings for the H3 core library. For available functions,

Kevin Schaich 12 Dec 24, 2022
The lastest all in one bombing tool coded in python uses tbomb api

BaapG-Attack is a python3 based script which is officially made for linux based distro . It is inbuit mass bomber with sms, mail, calls and many more bombing

59 Dec 25, 2022
Catalogue data - A Python Scripts to prepare catalogue data

catalogue_data Scripts to prepare catalogue data. Setup Clone this repo. Install

BigScience Workshop 3 Mar 03, 2022