A Snakemake workflow for standardised sc/snRNAseq analysis

Related tags

Miscellaneousbioinformaticssnakemakecondasingularityreproducible-sciencescrna-seq
Overview

single_snake_sequencing - sc/snRNAseq Snakemake Workflow

MIT License Status: Active CI/CD Codestyle: Black Codestyle: snakefmt

A Snakemake workflow for standardised sc/snRNAseq analysis.

Every single cell analysis is slightly different. This represents what I would call a "core" analysis, as nearly every analysis I perform start with something very akin to this. Given this custom nature of single cell, this workflow is not designed to be all encompassing. Rather, it aims to be extensible, modular, and reproducible. Any given step can be easily modified - as they are all self contained scripts - and a new rule can be easily added - see the downstream rules for an example. Finally, by taking advantage of the integrated Conda and Singularity support, we can run the whole thing in an isolated environment.

Notes on Installation

HOLDING

Notes on Configuration

⚠️ Be sure to change the configuration to suit your project!

For a full discussion of configuration, please see the configuration README.

Briefly, the general configuration file must be located at config/config.yaml. A samplesheet containing information pertaining to the data must be supplied as well. Both are schema validated.

Notes on Data

This pipeline expects de-multiplexed fastq.gz files, normally produced by some deriviative of bcl2fastq after sequencing. They can (technically) be placed anywhere, but we recommend creating a data directory in your project for them.

Notes on the tools

The analysis pipeline was run using Snakemake v6.6.1. The full version and software lists can be found under the relevant yaml files in workflow/envs. The all reasonable efforts have been made to ensure that the repository adheres to the best practices outlined here.

Notes on the analysis

For a full discussion on the analysis methods, please see the technical documentation.

Briefly, the count matrix was produced using Cellranger, droplet calling with DropletUtils::emptyDrops, doublet detection with SOLO from the scVI family, batch effect removal with harmonypy, and general analysis and data handling with scanpy.

Future work

  • Supply tests
  • Track lane in samples that have been pooled and de-multiplexed
  • Parallelise emptyDrops
  • Support custom references
  • Support SCTransform?
You might also like...
TickerRain is an open-source web app that stores and analysis Reddit posts in a transparent and semi-interactive manner.
TickerRain is an open-source web app that stores and analysis Reddit posts in a transparent and semi-interactive manner.

TickerRain is an open-source web app that stores and analysis Reddit posts in a transparent and semi-interactive manner

GonVas 180 Oct 8, 2022
Socorro is the Mozilla crash ingestion pipeline. It accepts and processes Breakpad-style crash reports. It provides analysis tools.

Socorro Socorro is a Mozilla-centric ingestion pipeline and analysis tools for crash reports using the Breakpad libraries. Support This is a Mozilla-s

Mozilla Services 552 Dec 19, 2022
frida-based ceserver. iOS analysis is possible with Cheat Engine.
frida-based ceserver. iOS analysis is possible with Cheat Engine.

frida-ceserver frida-based ceserver. iOS analysis is possible with Cheat Engine. Original by Dark Byte. Usage Install frida on iOS. python main.py Cyd

KenjiroIchise 89 Jan 8, 2023
This is an online course where you can learn and master the skill of low-level performance analysis and tuning.
This is an online course where you can learn and master the skill of low-level performance analysis and tuning.

Performance Ninja Class This is an online course where you can learn to find and fix low-level performance issues, for example CPU cache misses and br

Denis Bakhvalov 1.2k Dec 30, 2022
Cross-platform MachO/ObjC Static binary analysis tool & library. class-dump + otool + lipo + more

ktool Static Mach-O binary metadata analysis tool / information dumper pip3 install k2l Development is currently taking place on the @python3.10 branc

Kritanta 301 Dec 28, 2022
Some usefull scripts for the Nastran's 145 solution (Flutter Analysis) using the pyNastran package.
Some usefull scripts for the Nastran's 145 solution (Flutter Analysis) using the pyNastran package.

nastran-aero-flutter This project is intended to analyse the Supersonic Panel Flutter using the NASTRAN software. The project uses the pyNastran and t

zuckberj 11 Nov 16, 2022
Analysis of ROM image for Norsk Data VDU 301 S
Analysis of ROM image for Norsk Data VDU 301 S

This repository is meant to analyze the ROM images from Norsk Data VDU 301 S as provided at by Torfinn. To combine the two ROM image halves and extrac

Sebastian Rasmussen 1 Oct 21, 2021
Code needed for hybrid land cover change analysis for NASA IDS project

Documentation for the NASA IDS change analysis Poley 10/21/2021 Required python packages: whitebox numpy rasterio rasterio.mask os glob math itertools

Andrew Poley 2 Nov 12, 2021
Multifunctional Analysis of Regions through Input-Output

MARIO Multifunctional Analysis of Regions through Input-Output. (Documents) What is it MARIO is a python package for handling input-output tables and

null 14 Dec 25, 2022
Releases(v0.1.2)
Owner
IMS Bio2Core Facility
IMS Bio2Core Facility
GitHub Repository
addon for blender to import mocap data from tools like easymocap, frankmocap and Vibe

b3d_mocap_import addon for blender to import mocap data from tools like easymocap, frankmocap and Vibe ==================VIBE================== To use

Carlos Barreto 97 Dec 07, 2022
Python template for Advent of Code event

Advent of Code Python Starter A tamplate for Advent of Code write in Python. Usage The project use poetry for project manager. Clone this repository a

Leonardo Gago 6 Dec 31, 2022
A light library to build tiny websites

A light library to build tiny websites

BT.Q 1 Dec 23, 2021
Viewflow is an Airflow-based framework that allows data scientists to create data models without writing Airflow code.

Viewflow Viewflow is a framework built on the top of Airflow that enables data scientists to create materialized views. It allows data scientists to f

DataCamp 114 Oct 12, 2022
UUID_ApiGenerator - This an API that will return a key-value pair of randomly generated UUID

This an API that will return a key-value pair of randomly generated UUID. Key will be a timestamp and value will be UUID. While the

1 Jan 28, 2022
Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions

xbi Xbps-install wrapper written in Python that doesn't care about case sensitiveness and package versions. Description This Python script can be easi

Emanuele Sabato 5 Apr 11, 2022
Fetch PRs from GitHub and analyze which ones are unmergeable

Set up token Generate a personal access token on GitHub. Add repo permissions. export GH_TOKEN="abcdefg" Pull PR data make Usually, GitHub doesn't h

Stefan van der Walt 1 Nov 05, 2021
This alerts you when the avalanche score a goal

This alerts you when the avalanche score a goal

Davis Burrill 1 Jan 15, 2022
Easy installer for running Amazon AVS Device SDK on Raspberry Pi

avs-device-sdk-pi Scripts to enable Alexa voice activation using Picovoice Porcupine If you like the work, find it useful and if you would like to get

4 Nov 14, 2022
Start and stop your NiceHash miners using this script.

NiceHash Mining Scheduler Use this script to schedule your NiceHash Miner(s). Electricity costs between 4-9pm are high in my area and I want NiceHash

SeaRoth 2 Sep 30, 2022
An open source server for Super Mario Bros. 35

SMB35 A custom server for Super Mario Bros. 35 This server is highly experimental. Do not expect it to work without flaws.

Yannik Marchand 162 Dec 07, 2022
serological measurements from multiplexed ELISA assays

pysero pysero enables serological measurements with multiplexed and standard ELISA assays. The project automates estimation of antibody titers from da

Chan Zuckerberg Biohub 5 Aug 06, 2022
Expense Tracker is a very good tool to keep track of your expenseditures and the total money you saved.

Expense Tracker is a very good tool to keep track of your expenseditures and the total money you saved.

Shreejan Dolai 9 Dec 31, 2022
Audio2Face - a project that transforms audio to blendshape weights,and drives the digital human,xiaomei,in UE project

Audio2Face - a project that transforms audio to blendshape weights,and drives the digital human,xiaomei,in UE project

FACEGOOD 732 Jan 08, 2023
Turn your IPad into a Screen-Slaver with 1 simple Pythonista script

ScreenSlaver Turn your IPad into a Screen-Slaver with 1 simple Pythonista script

6 Jul 09, 2022
This script provides LIVE feedback for On-The-Fly data collection with RELION

README This script provides LIVE feedback for On-The-Fly data collection with RELION (very useful to explore already processed datasets too!) Creating

cryoEM CNIO 6 Jul 14, 2022
The program converts Swiss notes into American notes

Informatik-Programmieren Einleitung: Das Programm rechnet Schweizer Noten in das Amerikanische Noten um. Der Benutzer kann seine Note eingeben und der

2 Dec 16, 2021
Shopping-card - Shopping Card Project With Python

Shopping Card Project this application was built to handle problems with saving

moein98 1 May 06, 2022
A program that makes all 47 textures of Optifine CTM only using 2 textures

A program that makes all 47 textures of Optifine CTM only using 2 textures

1 Jan 22, 2022
combs is a package used to generate all possible combinations of a given length k on a given set.

The package combs is a package used to generate all possible combinations of a given length k on a given set. The set is given as a list, and k must b

1 Dec 24, 2021