Pca-on-genotypes - Mini bioinformatics project - PCA on genotypes

Related tags

Deep Learningpca-on-genotypes
Overview

Mini bioinformatics project: PCA on genotypes

This repo contains the code from this video: https://youtu.be/-PCKK_nwFdA

If you somehow end up publishing a paper based on this type of project, you should cite this original paper it was inspired by: https://www.nature.com/articles/nature07331

URLs to download files

curl -O ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz

curl -O ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi

curl -O ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel

# Faster downloads through AWS:

curl -O https://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz

curl -O https://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi

curl -O https://1000genomes.s3.amazonaws.com/release/20110521/phase1_integrated_calls.20101123.ALL.panel

# or use "wget" instead of "curl -O" if you don't have curl.

Colab notebook:

https://colab.research.google.com/drive/1o24ZfqDoBEwvRSx_Br1u7edPPXLLx4w7?usp=sharing

Owner
Maria Nattestad
On the Genomics team in Google Health. PhD from Cold Spring Harbor Laboratory.
Maria Nattestad
GitHub Repository
Learning trajectory representations using self-supervision and programmatic supervision.

Trajectory Embedding for Behavior Analysis (TREBA) Implementation from the paper: Jennifer J. Sun, Ann Kennedy, Eric Zhan, David J. Anderson, Yisong Y

58 Jan 06, 2023
This repository contains numerical implementation for the paper Intertemporal Pricing under Reference Effects: Integrating Reference Effects and Consumer Heterogeneity.

This repository contains numerical implementation for the paper Intertemporal Pricing under Reference Effects: Integrating Reference Effects and Consumer Heterogeneity.

Hansheng Jiang 6 Nov 18, 2022
Awesome Long-Tailed Learning

Awesome Long-Tailed Learning This repo pays specially attention to the long-tailed distribution, where labels follow a long-tailed or power-law distri

Stomach_ache 284 Jan 06, 2023
PyTorch implementation for NED. It can be used to manipulate the facial emotions of actors in videos based on emotion labels or reference styles.

Neural Emotion Director (NED) - Official Pytorch Implementation Example video of facial emotion manipulation while retaining the original mouth motion

Foivos Paraperas 89 Dec 23, 2022
Official implementation of "Membership Inference Attacks Against Self-supervised Speech Models"

Introduction Official implementation of "Membership Inference Attacks Against Self-supervised Speech Models". In this work, we demonstrate that existi

Wei-Cheng Tseng 7 Nov 01, 2022
Neural Articulated Radiance Field

Neural Articulated Radiance Field NARF Neural Articulated Radiance Field Atsuhiro Noguchi, Xiao Sun, Stephen Lin, Tatsuya Harada ICCV 2021 [Paper] [Co

Atsuhiro Noguchi 144 Jan 03, 2023
这是一个yolox-keras的源码，可以用于训练自己的模型。

YOLOX：You Only Look Once目标检测模型在Keras当中的实现 目录 性能情况 Performance 实现的内容 Achievement 所需环境 Environment 小技巧的设置 TricksSet 文件下载 Download 训练步骤 How2train 预测步骤 Ho

Bubbliiiing 64 Nov 10, 2022
Sub-tomogram-Detection - Deep learning based model for Cyro ET Sub-tomogram-Detection

Deep learning based model for Cyro ET Sub-tomogram-Detection High degree of stru

Siddhant Kumar 2 Feb 04, 2022
Python Algorithm Interview Book Review

파이썬 알고리즘 인터뷰 책 리뷰 리뷰 IT 대기업에 들어가고 싶은 목표가 있다. 내가 꿈꿔온 회사에서 일하는 사람들의 모습을 보면 멋있다고 생각이 들고 나의 목표에 대한 열망이 강해지는 것 같다. 미래의 핵심 사업 중 하나인 SW 부분을 이끌고 발전시키는 우리나라의 I

SharkBSJ 1 Dec 14, 2021
AbelNN: Deep Learning Python module from scratch

AbelNN: Deep Learning Python module from scratch I have implemented several neural networks from scratch using only Numpy. I have designed the module

Abel 2 Apr 12, 2022
Deep-Learning-Image-Captioning - Implementing convolutional and recurrent neural networks in Keras to generate sentence descriptions of images

Deep Learning - Image Captioning with Convolutional and Recurrent Neural Nets ========================================================================

23 Apr 06, 2022
Iris prediction model is used to classify iris species created julia's DecisionTree, DataFrames, JLD2, PlotlyJS and Statistics packages.

Iris Species Predictor Iris prediction is used to classify iris species using their sepal length, sepal width, petal length and petal width created us

Siva Prakash 2 Jan 06, 2022
IEEE Winter Conference on Applications of Computer Vision 2022 Accepted

SSKT(Accepted WACV2022) Concept map Dataset Image dataset CIFAR10 (torchvision) CIFAR100 (torchvision) STL10 (torchvision) Pascal VOC (torchvision) Im

1 Nov 17, 2022
A novel Engagement Detection with Multi-Task Training (ED-MTT) system

A novel Engagement Detection with Multi-Task Training (ED-MTT) system which minimizes MSE and triplet loss together to determine the engagement level of students in an e-learning environment.

Onur Çopur 12 Nov 11, 2022
DEMix Layers for Modular Language Modeling

DEMix This repository contains modeling utilities for "DEMix Layers: Disentangling Domains for Modular Language Modeling" (Gururangan et. al, 2021). T

Suchin 43 Nov 11, 2022
A vanilla 3D face modeling on pose-invariant and multi-lightning image data

3D-Face-Modeling A vanilla 3D face modeling on pose-invariant and multi-lightning image data Table of Contents Background Install Usage Contributing B

Haochen Zhang 1 Mar 12, 2022
BasicVSR++: Improving Video Super-Resolution with Enhanced Propagation and Alignment

BasicVSR++: Improving Video Super-Resolution with Enhanced Propagation and Alignment

Holy Wu 35 Jan 01, 2023
Generic Event Boundary Detection: A Benchmark for Event Segmentation

Generic Event Boundary Detection: A Benchmark for Event Segmentation We release our data annotation & baseline codes for detecting generic event bound

47 Nov 22, 2022
A unified framework to jointly model images, text, and human attention traces.

connect-caption-and-trace This repository contains the reference code for our paper Connecting What to Say With Where to Look by Modeling Human Attent

Meta Research 73 Oct 24, 2022
Morphable Detector for Object Detection on Demand

Morphable Detector for Object Detection on Demand (ICCV 2021) PyTorch implementation of the paper Morphable Detector for Object Detection on Demand. I

9 Feb 23, 2022