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
An attempt at the implementation of GLOM, Geoffrey Hinton's paper for emergent part-whole hierarchies from data

GLOM TensorFlow This Python package attempts to implement GLOM in TensorFlow, which allows advances made by several different groups transformers, neu

Rishit Dagli 32 Feb 21, 2022
NDE: Climate Modeling with Neural Diffusion Equation, ICDM'21

Climate Modeling with Neural Diffusion Equation Introduction This is the repository of our accepted ICDM 2021 paper "Climate Modeling with Neural Diff

Jeehyun Hwang 5 Dec 18, 2022
Unifying Global-Local Representations in Salient Object Detection with Transformer

GLSTR (Global-Local Saliency Transformer) This is the official implementation of paper "Unifying Global-Local Representations in Salient Object Detect

11 Aug 24, 2022
🎓Automatically Update CV Papers Daily using Github Actions (Update at 12:00 UTC Every Day)

🎓Automatically Update CV Papers Daily using Github Actions (Update at 12:00 UTC Every Day)

Realcat 270 Jan 07, 2023
PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud, CVPR 2019.

PointRCNN PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud Code release for the paper PointRCNN:3D Object Proposal Generation a

Shaoshuai Shi 1.5k Dec 27, 2022
[ICLR2021oral] Rethinking Architecture Selection in Differentiable NAS

DARTS-PT Code accompanying the paper ICLR'2021: Rethinking Architecture Selection in Differentiable NAS Ruochen Wang, Minhao Cheng, Xiangning Chen, Xi

Ruochen Wang 86 Dec 27, 2022
Deep Image Search is an AI-based image search engine that includes deep transfor learning features Extraction and tree-based vectorized search.

Deep Image Search - AI-Based Image Search Engine Deep Image Search is an AI-based image search engine that includes deep transfer learning features Ex

139 Jan 01, 2023
UDP++ (ECCVW 2020 Oral), (Winner of COCO 2020 Keypoint Challenge).

UDP-Pose This is the pytorch implementation for UDP++, which won the Fisrt place in COCO Keypoint Challenge at ECCV 2020 Workshop. Top-Down Results on

20 Jul 29, 2022
Finite-temperature variational Monte Carlo calculation of uniform electron gas using neural canonical transformation.

CoulombGas This code implements the neural canonical transformation approach to the thermodynamic properties of uniform electron gas. Building on JAX,

FermiFlow 9 Mar 03, 2022
O2O-Afford: Annotation-Free Large-Scale Object-Object Affordance Learning (CoRL 2021)

O2O-Afford: Annotation-Free Large-Scale Object-Object Affordance Learning Object-object Interaction Affordance Learning. For a given object-object int

Kaichun Mo 26 Nov 04, 2022
details on efforts to dump the Watermelon Games Paprium cart

Reminder, if you like these repos, fork them so they don't disappear https://github.com/ArcadeHustle/WatermelonPapriumDump/fork Big thanks to Fonzie f

Hustle Arcade 29 Dec 11, 2022
EdiBERT, a generative model for image editing

EdiBERT, a generative model for image editing EdiBERT is a generative model based on a bi-directional transformer, suited for image manipulation. The

16 Dec 07, 2022
LaBERT - A length-controllable and non-autoregressive image captioning model.

Length-Controllable Image Captioning (ECCV2020) This repo provides the implemetation of the paper Length-Controllable Image Captioning. Install conda

bearcatt 53 Nov 13, 2022
Code, Models and Datasets for OpenViDial Dataset

OpenViDial This repo contains downloading instructions for the OpenViDial dataset in 《OpenViDial: A Large-Scale, Open-Domain Dialogue Dataset with Vis

119 Dec 08, 2022
TabNet for fastai

TabNet for fastai This is an adaptation of TabNet (Attention-based network for tabular data) for fastai (=2.0) library. The original paper https://ar

Mikhail Grankin 116 Oct 21, 2022
ISBI 2022: Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image.

Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Introduction This repository contains the PyTorch implem

25 Nov 09, 2022
Human Action Controller - A human action controller running on different platforms.

Human Action Controller (HAC) Goal A human action controller running on different platforms. Fun Easy-to-use Accurate Anywhere Fun Examples Mouse Cont

27 Jul 20, 2022
KIND: an Italian Multi-Domain Dataset for Named Entity Recognition

KIND (Kessler Italian Named-entities Dataset) KIND is an Italian dataset for Named-Entity Recognition. It contains more than one million tokens with t

Digital Humanities 5 Jun 21, 2022
Decompose to Adapt: Cross-domain Object Detection via Feature Disentanglement

Decompose to Adapt: Cross-domain Object Detection via Feature Disentanglement In this project, we proposed a Domain Disentanglement Faster-RCNN (DDF)

19 Nov 24, 2022
BasicVSR: The Search for Essential Components in Video Super-Resolution and Beyond

BasicVSR BasicVSR: The Search for Essential Components in Video Super-Resolution and Beyond Ported from https://github.com/xinntao/BasicSR Dependencie

Holy Wu 8 Jun 07, 2022