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
PyTorch code for BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation

BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation

Salesforce 1.3k Dec 31, 2022
Unofficial Implement PU-Transformer

PU-Transformer-pytorch Pytorch unofficial implementation of PU-Transformer (PU-Transformer: Point Cloud Upsampling Transformer) https://arxiv.org/abs/

Lee Hyung Jun 7 Sep 21, 2022
Unsupervised phone and word segmentation using dynamic programming on self-supervised VQ features.

Unsupervised Phone and Word Segmentation using Vector-Quantized Neural Networks Overview Unsupervised phone and word segmentation on speech data is pe

Herman Kamper 13 Dec 11, 2022
Generate pixel-style avatars with python.

face2pixel Generate pixel-style avatars with python. Run: Clone the project: git clone https://github.com/theodorecooper/face2pixel install requiremen

Theodore Cooper 2 May 11, 2022
ROSITA: Enhancing Vision-and-Language Semantic Alignments via Cross- and Intra-modal Knowledge Integration

ROSITA News & Updates (24/08/2021) Release the demo to perform fine-grained semantic alignments using the pretrained ROSITA model. (15/08/2021) Releas

Vision and Language Group@ MIL 48 Dec 23, 2022
Collection of Docker images for ML/DL and video processing projects

Collection of Docker images for ML/DL and video processing projects. Overview of images Three types of images differ by tag postfix: base: Python with

OSAI 87 Nov 22, 2022
Face Recognition plus identification simply and fast | Python

PyFaceDetection Face Recognition plus identification simply and fast Ubuntu Setup sudo pip3 install numpy sudo pip3 install cmake sudo pip3 install dl

Peyman Majidi Moein 16 Sep 22, 2022
PartImageNet is a large, high-quality dataset with part segmentation annotations

PartImageNet: A Large, High-Quality Dataset of Parts We will release our dataset and scripts soon after cleaning and approval. Introduction PartImageN

Ju He 77 Nov 30, 2022
ALIbaba's Collection of Encoder-decoders from MinD (Machine IntelligeNce of Damo) Lab

AliceMind AliceMind: ALIbaba's Collection of Encoder-decoders from MinD (Machine IntelligeNce of Damo) Lab This repository provides pre-trained encode

Alibaba 1.4k Jan 01, 2023
An 16kHz implementation of HiFi-GAN for soft-vc.

HiFi-GAN An 16kHz implementation of HiFi-GAN for soft-vc. Relevant links: Official HiFi-GAN repo HiFi-GAN paper Soft-VC repo Soft-VC paper Example Usa

Benjamin van Niekerk 42 Dec 27, 2022
Unofficial pytorch implementation of 'Image Inpainting for Irregular Holes Using Partial Convolutions'

pytorch-inpainting-with-partial-conv Official implementation is released by the authors. Note that this is an ongoing re-implementation and I cannot f

Naoto Inoue 525 Jan 01, 2023
Oscar and VinVL

Oscar: Object-Semantics Aligned Pre-training for Vision-and-Language Tasks VinVL: Revisiting Visual Representations in Vision-Language Models Updates

Microsoft 938 Dec 26, 2022
Preprocessed Datasets for our Multimodal NER paper

Unified Multimodal Transformer (UMT) for Multimodal Named Entity Recognition (MNER) Two MNER Datasets and Codes for our ACL'2020 paper: Improving Mult

76 Dec 21, 2022
Automatic packaging of the open-composite libs for OvGME

OvGME Packager for OpenXR – OpenComposite for DCS Note This repository is currently unsupported and needs to be migrated to the upstream OpenComposite

12 Nov 03, 2022
nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures.

nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures. Here you will find the scripts necessary to produce th

Jesse Willis 0 Jan 20, 2022
A Temporal Extension Library for PyTorch Geometric

Documentation | External Resources | Datasets PyTorch Geometric Temporal is a temporal (dynamic) extension library for PyTorch Geometric. The library

Benedek Rozemberczki 1.9k Jan 07, 2023
GMFlow: Learning Optical Flow via Global Matching

GMFlow GMFlow: Learning Optical Flow via Global Matching Authors: Haofei Xu, Jing Zhang, Jianfei Cai, Hamid Rezatofighi, Dacheng Tao We streamline the

Haofei Xu 298 Jan 04, 2023
Code for the paper "Reinforcement Learning as One Big Sequence Modeling Problem"

Trajectory Transformer Code release for Reinforcement Learning as One Big Sequence Modeling Problem. Installation All python dependencies are in envir

Michael Janner 269 Jan 05, 2023
PyTorch implementation of Trust Region Policy Optimization

PyTorch implementation of TRPO Try my implementation of PPO (aka newer better variant of TRPO), unless you need to you TRPO for some specific reasons.

Ilya Kostrikov 366 Nov 15, 2022
Repository containing the PhD Thesis "Formal Verification of Deep Reinforcement Learning Agents"

Getting Started This repository contains the code used for the following publications: Probabilistic Guarantees for Safe Deep Reinforcement Learning (

Edoardo Bacci 5 Aug 31, 2022