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
🦕 NanoSaur is a little tracked robot ROS2 enabled, made for an NVIDIA Jetson Nano

🦕 nanosaur NanoSaur is a little tracked robot ROS2 enabled, made for an NVIDIA Jetson Nano Website: nanosaur.ai Do you need an help? Discord For tech

NanoSaur 162 Dec 09, 2022
PyTorch wrappers for using your model in audacity!

audacitorch This package contains utilities for prepping PyTorch audio models for use in Audacity. More specifically, it provides abstract classes for

Hugo Flores García 130 Dec 14, 2022
This repository contains the code for the paper in EMNLP 2021: "HRKD: Hierarchical Relational Knowledge Distillation for Cross-domain Language Model Compression".

HRKD: Hierarchical Relational Knowledge Distillation for Cross-domain Language Model Compression This repository contains the code for the paper in EM

Chenhe Dong 2 Mar 24, 2022
Official implementation of Self-supervised Image-to-text and Text-to-image Synthesis

Self-supervised Image-to-text and Text-to-image Synthesis This is the official implementation of Self-supervised Image-to-text and Text-to-image Synth

6 Jul 31, 2022
State of the art Semantic Sentence Embeddings

Contrastive Tension State of the art Semantic Sentence Embeddings Published Paper · Huggingface Models · Report Bug Overview This is the official code

Fredrik Carlsson 88 Dec 30, 2022
A library for answering questions using data you cannot see

A library for computing on data you do not own and cannot see PySyft is a Python library for secure and private Deep Learning. PySyft decouples privat

OpenMined 8.5k Jan 02, 2023
Global-Local Attention for Emotion Recognition

Global-Local Attention for Emotion Recognition Requirements Python 3 Install tensorflow (or tensorflow-gpu) = 2.0.0 Install some other packages pip i

Minh Nhat Le 15 Apr 21, 2022
Few-Shot Object Detection via Association and DIscrimination

Few-Shot Object Detection via Association and DIscrimination Code release of our NeurIPS 2021 paper: Few-Shot Object Detection via Association and DIs

Cao Yuhang 49 Dec 18, 2022
Code for ICMI2020 and ICMI2021 papers: "Studying Person-Specific Pointing and Gaze Behavior for Multimodal Referencing of Outside Objects from a Moving Vehicle" and "ML-PersRef: A Machine Learning-based Personalized Multimodal Fusion Approach for Referencing Outside Objects From a Moving Vehicle"

ML-PersRef This repository has python code (in jupyter notebooks) for both of the following papers: ML-PersRef: A Machine Learning-based Personalized

3 Sep 04, 2022
Learning Open-World Object Proposals without Learning to Classify

Learning Open-World Object Proposals without Learning to Classify Pytorch implementation for "Learning Open-World Object Proposals without Learning to

Dahun Kim 149 Dec 22, 2022
A 3D Dense mapping backend library of SLAM based on taichi-Lang designed for the aerial swarm.

TaichiSLAM This project is a 3D Dense mapping backend library of SLAM based Taichi-Lang, designed for the aerial swarm. Intro Taichi is an efficient d

XuHao 230 Dec 19, 2022
The `rtdl` library + The official implementation of the paper

The `rtdl` library + The official implementation of the paper "Revisiting Deep Learning Models for Tabular Data"

Yandex Research 510 Dec 30, 2022
Python utility to generate filesystem content for Obsidian.

Security Vault Generator Quickly parse, format, and output common frameworks/content for Obsidian.md. There is a strong focus on MITRE ATT&CK because

Justin Angel 73 Dec 02, 2022
Ansible Automation Example: JSNAPY PRE/POST Upgrade Validation

Ansible Automation Example: JSNAPY PRE/POST Upgrade Validation Overview This example will show how to validate the status of our firewall before and a

Calvin Remsburg 1 Jan 07, 2022
Scalable Optical Flow-based Image Montaging and Alignment

SOFIMA SOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool for stitching, aligning and warping large 2d, 3d and 4d microscopy

Google Research 16 Dec 21, 2022
Back to the Feature: Learning Robust Camera Localization from Pixels to Pose (CVPR 2021)

Back to the Feature with PixLoc We introduce PixLoc, a neural network for end-to-end learning of camera localization from an image and a 3D model via

Computer Vision and Geometry Lab 610 Jan 05, 2023
Breaking Shortcut: Exploring Fully Convolutional Cycle-Consistency for Video Correspondence Learning

Breaking Shortcut: Exploring Fully Convolutional Cycle-Consistency for Video Correspondence Learning Yansong Tang *, Zhenyu Jiang *, Zhenda Xie *, Yue

Zhenyu Jiang 12 Nov 16, 2022
learning and feeling SLAM together with hands-on-experiments

modern-slam-tutorial-python Learning and feeling SLAM together with hands-on-experiments 😀 😃 😆 Dependencies Most of the examples are based on GTSAM

Giseop Kim 59 Dec 22, 2022
toroidal - a lightweight transformer library for PyTorch

toroidal - a lightweight transformer library for PyTorch Toroidal transformers are of smaller size and lower weight than the more common E-I types. Th

MathInf GmbH 64 Jan 07, 2023
List some popular DeepFake models e.g. DeepFake, FaceSwap-MarekKowal, IPGAN, FaceShifter, FaceSwap-Nirkin, FSGAN, SimSwap, CihaNet, etc.

deepfake-models List some popular DeepFake models e.g. DeepFake, CihaNet, SimSwap, FaceSwap-MarekKowal, IPGAN, FaceShifter, FaceSwap-Nirkin, FSGAN, Si

Mingcan Xiang 100 Dec 17, 2022