Python implementation of MULTIseq barcode alignment using fuzzy string matching and GMM barcode assignment

Overview

py-multi-seq

Python implementation of MULTIseq barcode alignment using fuzzy string matching and GMM barcode assignment.

The scripts in this repository are roughly analogous to the provided MULTI-seq R package deMULTIplex at https://github.com/chris-mcginnis-ucsf/MULTI-seq. This script loads read data from paired end reads, performs fuzzy string matching from paired end reads to the provided MULTIseq barcode file, then counts the reads mapping to each barcode. Next, Expectation Maximization is used to fit Gaussian Mixture Models for each barcode, which assigns each cell a most likely barcode, no barcode or doublet barcodes.

Installation

Clone this repository. The scripts within also depend on python >= 3.7 and the following packages which can be installed with: pip install pandas numpy scipy fuzzywuzzy tqdm sparse_dot_topn scanpy natsort

You will need the cellranger cell barcodes file before running. You can in theory modify the MultiseqIndices.txt along with the read length parameters for custom barcodes in the reads.

Usage example for 10X scRNAseq or Multiome + MULTIseq:

python BarcodeFuzzyMatching.py /path/to/this/repo/MultiseqSamplesExample.txt /path/to/this/repo/MultiseqIndices.txt /path/to/sampleMULTIseq_R1.fastq /path/to/cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz /path/to/output/dir/ 16 8 0

python RunDemuxEM.py /path/to/output/dir/ /path/to/cellranger/outs/filtered_feature_bc_matrix/

Running this pipeline will output a matrix of barcodes by reads_counts, as well as a csv listing cell barcodes and their assigned barcode(s).

Owner
MT Schmitz
Matthew Schmitz Developmental and Stem Cell Biology Graduate Student at UCSF
MT Schmitz
Nerf pl - NeRF (Neural Radiance Fields) and NeRF in the Wild using pytorch-lightning

nerf_pl Update: an improved NSFF implementation to handle dynamic scene is open! Update: NeRF-W (NeRF in the Wild) implementation is added to nerfw br

AI葵 1.8k Dec 30, 2022
The official implementation of paper Siamese Transformer Pyramid Networks for Real-Time UAV Tracking, accepted by WACV22

SiamTPN Introduction This is the official implementation of the SiamTPN (WACV2022). The tracker intergrates pyramid feature network and transformer in

Robotics and Intelligent Systems Control @ NYUAD 29 Jan 08, 2023
A Simple Framwork for CV Pre-training Model (SOCO, VirTex, BEiT)

A Simple Framwork for CV Pre-training Model (SOCO, VirTex, BEiT)

Sense-GVT 14 Jul 07, 2022
Noise Conditional Score Networks (NeurIPS 2019, Oral)

Generative Modeling by Estimating Gradients of the Data Distribution This repo contains the official implementation for the NeurIPS 2019 paper Generat

451 Dec 26, 2022
A Pytorch implementation of MoveNet from Google. Include training code and pre-train model.

Movenet.Pytorch Intro MoveNet is an ultra fast and accurate model that detects 17 keypoints of a body. This is A Pytorch implementation of MoveNet fro

Mr.Fire 241 Dec 26, 2022
Code and data to accompany the camera-ready version of "Cross-Attention is All You Need: Adapting Pretrained Transformers for Machine Translation" in EMNLP 2021

Code and data to accompany the camera-ready version of "Cross-Attention is All You Need: Adapting Pretrained Transformers for Machine Translation" in EMNLP 2021

Mozhdeh Gheini 16 Jul 16, 2022
Implementation of "DeepOrder: Deep Learning for Test Case Prioritization in Continuous Integration Testing".

DeepOrder Implementation of DeepOrder for the paper "DeepOrder: Deep Learning for Test Case Prioritization in Continuous Integration Testing". Project

6 Nov 07, 2022
Instant-nerf-pytorch - NeRF trained SUPER FAST in pytorch

instant-nerf-pytorch This is WORK IN PROGRESS, please feel free to contribute vi

94 Nov 22, 2022
PyTorch implementation of "Learning to Discover Cross-Domain Relations with Generative Adversarial Networks"

DiscoGAN in PyTorch PyTorch implementation of Learning to Discover Cross-Domain Relations with Generative Adversarial Networks. * All samples in READM

Taehoon Kim 1k Jan 04, 2023
deep_image_prior_extension

Code for "Is Deep Image Prior in Need of a Good Education?" Project page: https://jleuschn.github.io/docs.educated_deep_image_prior/. Supplementary Ma

riccardo barbano 7 Jan 09, 2022
K Closest Points and Maximum Clique Pruning for Efficient and Effective 3D Laser Scan Matching (To appear in RA-L 2022)

KCP The official implementation of KCP: k Closest Points and Maximum Clique Pruning for Efficient and Effective 3D Laser Scan Matching, accepted for p

Yu-Kai Lin 109 Dec 14, 2022
TensorFlow implementation of ENet

TensorFlow-ENet TensorFlow implementation of ENet: A Deep Neural Network Architecture for Real-Time Semantic Segmentation. This model was tested on th

Kwotsin 255 Oct 17, 2022
Dilated RNNs in pytorch

PyTorch Dilated Recurrent Neural Networks PyTorch implementation of Dilated Recurrent Neural Networks (DilatedRNN). Getting Started Installation: $ pi

Zalando Research 200 Nov 17, 2022
Progressive Image Deraining Networks: A Better and Simpler Baseline

Progressive Image Deraining Networks: A Better and Simpler Baseline [arxiv] [pdf] [supp] Introduction This paper provides a better and simpler baselin

190 Dec 01, 2022
Pytorch Implementation of Spiking Neural Networks Calibration, ICML 2021

SNN_Calibration Pytorch Implementation of Spiking Neural Networks Calibration, ICML 2021 Feature Comparison of SNN calibration: Features SNN Direct Tr

Yuhang Li 60 Dec 27, 2022
From this paper "SESNet: A Semantically Enhanced Siamese Network for Remote Sensing Change Detection"

SESNet for remote sensing image change detection It is the implementation of the paper: "SESNet: A Semantically Enhanced Siamese Network for Remote Se

1 May 24, 2022
Bayesian optimisation library developped by Huawei Noah's Ark Library

Bayesian Optimisation Research This directory contains official implementations for Bayesian optimisation works developped by Huawei R&D, Noah's Ark L

HUAWEI Noah's Ark Lab 395 Dec 30, 2022
Breaking the Dilemma of Medical Image-to-image Translation

Breaking the Dilemma of Medical Image-to-image Translation Supervised Pix2Pix and unsupervised Cycle-consistency are two modes that dominate the field

Kid Liet 86 Dec 21, 2022
Compare outputs between layers written in Tensorflow and layers written in Pytorch

Compare outputs of Wasserstein GANs between TensorFlow vs Pytorch This is our testing module for the implementation of improved WGAN in Pytorch Prereq

Hung Nguyen 72 Dec 20, 2022
PyTorch code for SENTRY: Selective Entropy Optimization via Committee Consistency for Unsupervised DA

PyTorch Code for SENTRY: Selective Entropy Optimization via Committee Consistency for Unsupervised Domain Adaptation Viraj Prabhu, Shivam Khare, Deeks

Viraj Prabhu 46 Dec 24, 2022