limix/pandas-plink

PLINK reader for Python.

Language: Python - Size: 2.21 MB - Last synced at: 6 days ago - Pushed at: 10 days ago - Stars: 86 - Forks: 21

esohkevin/ei-gwas

gwas workflow from raw intensity data to in-silico functional mapping

Language: Shell - Size: 709 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 3 - Forks: 0

Computational-Genomics-BSC/plink-bed-reader

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.

Language: Python - Size: 3.96 MB - Last synced at: 28 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

NajlaAbassi/ROHStats

🧬 ROHStats: Fast and easy ROH statistics and visualization from PLINK outputs

Language: R - Size: 11.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

shanecrinion/causal-inference

Mendelian randomisation analysis using GWAS data for neuropsychiatric disorders and chronotype to assess their bidirectional causal relationship.

Language: R - Size: 1.29 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

cnr-ibba/nf-neestimator

A nextflow pipeline for Current Effective Population Size (Ne) calculations with bootstrapping

Language: Nextflow - Size: 159 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

OrangePomeranian/Master_thesis

Analysis of SNPs that have the greatest impact of appearance of mammary gland tumour in dogs.

Language: R - Size: 17 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

OpenMendel/SnpArrays.jl

Compressed storage for SNP data

Language: Julia - Size: 8.5 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 45 - Forks: 9

NCI-CGR/GwasQcPipeline

The CGR GWAS QC processing workflow.

Language: Python - Size: 89.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 2

milescsmith/PLINKLiftOver

Perform liftover on plink files

Language: Python - Size: 242 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 5 - Forks: 1

ThWacker/Data_Steward_Assignment

Repository accompanying the task given for the Data Steward position interview

Language: Python - Size: 127 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ahmedmoustafa/genetic-ancestry

Genetic Ancestry

Language: Jupyter Notebook - Size: 13.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

AJResearchGroup/plinkr

Work with PLINK from R

Language: R - Size: 6.46 MB - Last synced at: 6 months ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 2

krassowski/jupyter-locuszoom

LocusZoom in Jupyter notebooks

Language: TypeScript - Size: 482 KB - Last synced at: 3 days ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Language: C - Size: 7.99 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 30 - Forks: 12

QuantGen/BEDMatrix

A matrix-like wrapper around PLINK .bed files

Language: C - Size: 1.84 MB - Last synced at: 16 days ago - Pushed at: 9 months ago - Stars: 18 - Forks: 2

kostapc/Putty-Tunnel-Manager

Fixes and new release. PuTTY Tunnel Manager allows you to easily open tunnels, that are defined in a PuTTY session, from the system tray. You can also move the tunnels from PuTTY to PuTTY Tunnel Manager. This allows you to use PuTTY just for SSH shell sessions (without opening tunnels), and use PuTTY Tunnel Manager just for tunneling.

Language: C# - Size: 916 KB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 59 - Forks: 12

cnr-ibba/SMARTER-database

Smarter database repository

Language: Jupyter Notebook - Size: 1.43 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

esohkevin/esohkevin.github.io

esohinformatics

Size: 25.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

jlc-christie/plink2merlin

Command Line Python Utility to convert from plink format to Abecasis Lab's QTDT format (used by Merlin).

Language: Python - Size: 18.6 KB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 3

CarolinaPB/population-structural-var-calling-smoove

population structural variant calling with smoove

Language: Python - Size: 1.84 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 3

kenhanscombe/plink-custom-r

Setup and starter script for the PLINK R plugin.

Language: R - Size: 238 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 7 - Forks: 0

insilico/inbix

In Silico Bioinformatics Toolbox

Language: C++ - Size: 10.2 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

tojojames/PhaseImpute

EXAMPLE CODE IMPUTATION WITH ONE PHASED REFERENCE PANEL FROM PLINK FILES

Language: R - Size: 925 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

imyingchulo/gprs

Language: Python - Size: 556 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

Buycasinos/CRYPTO-CASINO-SITE

This is our premade Crypto Gambling / Casino site - https://t.me/buycasinos

Language: PHP - Size: 2.93 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

OrangePomeranian/Quantitative_Genetics

Language: R - Size: 779 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

hwittich/Benchmarking_Pop_Structure_Tools

BIOI500 - Advanced Bioinformatics final project at Loyola University Chicago.

Size: 643 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

MareesAT/GWA_tutorial

A comprehensive tutorial about GWAS and PRS

Size: 31 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 695 - Forks: 301

adiamb/Remove-duplicate-snps-plink

A python script to remove duplicate snps from plink files and recode the resultant files into plink binaries free of duplicate snps

Language: Python - Size: 18.6 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

uroesch/PlinkProxyPortable

PlinkProxy for PortableApps.com

Language: PowerShell - Size: 414 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

npredey/GeneticAncestryTool

Language: Python - Size: 34.5 MB - Last synced at: about 1 month ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 3

ECRRM/genomics-commons

Genomics Commons

Language: Jupyter Notebook - Size: 2.75 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

quartzbio/plinker_pkg 📦

plinker is a R package to interface PLINK over PLINK BED files.

Language: R - Size: 2.25 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

esohkevin/gwas-tips

tips and tricks in genome-wide association studies - a tutorial

Size: 19.1 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 8

ACAD-UofA/Guide-to-manipulating-PLINK-EIG-and-VCF-files

A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

Language: Shell - Size: 128 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 1

anilprakash94/agaat

Automated Tool for Global Screening Array analysis

Language: Python - Size: 108 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 0

uroesch/PlinkProxy

Windows frontend for digging SSH tunnels and creating socks proxies

Language: AutoIt - Size: 159 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

ikmb/gwas-assoc

The IKMB GWAS Association Testing Pipeline

Language: Python - Size: 2.34 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 1

svpipaliya/GWAS-scripts

Bash scripts provided here to run various GWAS QC, Imputation, PCA, and association testing steps using PLINK, SMARTPCA, RStats and Visualization

Language: R - Size: 24.4 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Chris1221/pRs 📦

Toolkit for the efficient construction and analysis of polygenic risk scores in R.

Language: R - Size: 10.9 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 7

rootstrap/ImputationGeneris Fork of asiadmitchell/ImputationGeneris 📦

DNA Imputation tool for Generis.

Language: R - Size: 5.56 MB - Last synced at: 8 days ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 1

solelena/PSReliP

An integrated pipeline for analysis and visualization of Population Structure and Relatedness based on genome-wide genetic variant data

Language: R - Size: 168 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

Vegz78/PS3FromWin

Script package to automate waking and playing your PS3 from your (remote) Windows PC

Language: Batchfile - Size: 14.6 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 1

hclivess/sshauto

Automate repetitive Putty/SSH tasks, a free alternative to Ansible

Language: Python - Size: 426 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 0

kalilamali/FishDNA_pipeline

Step-by-step approach in the analysis of Rainbow trout DNA from raw reads to population insights using fastqc, trimmomatic, bwa, vcftools, plink, and R.

Size: 10.6 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

georgiesamaha/ProbeRemap

Map SNP positions to a supplied reference assembly using BLAST. Filter results for best hit. Output in plink format.

Language: Python - Size: 118 KB - Last synced at: 2 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

acostauribe/Plink_tutorial

This is a short Plink tutorial I developed as a markdown for my students in the Research Mentorship Program at UCSB

Size: 2.93 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

arizvisa/ansible Fork of ansible/ansible

So, ansible is some pretty fucked code. It's got some really bad hacks, and the authors didn't understand that python offers some elegant and portable ways of doing some of the things that they do. Anyways, this is my port of ansible to native windows. It uses plink.exe for doing ssh connections, so put that somewhere in your path. You're welcome. -- NEWS : As expected, this project died because I lost interest in ansible and found something significantly better.

Language: Python - Size: 28.4 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

roshchupkin/py4plink

Python library to work with PLINK files.

Language: Python - Size: 3.91 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

adRn-s/deskPlink

Shiny GUI for PLINK, a variant association analysis toolset.

Language: R - Size: 81.1 KB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

benknoble/plink

The DSL for Dotfiles

Language: Perl - Size: 39.1 KB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

karatugo/sm-basic-2

Very basic Snakemake workflow

Language: Python - Size: 7.81 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

MikeDacre/LDDirection

Get information about direction of agreement for any two lists of SNPs, based on LDlink and plink

Language: Python - Size: 112 KB - Last synced at: about 5 hours ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

eliorav/Biology-Tools

A docker wrapper for plink

Language: Dockerfile - Size: 17.6 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

ammodramus/microplink

Fast and minimal PLINK file processing with numba

Language: Python - Size: 3.91 KB - Last synced at: 28 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

benknoble/vim-plink

Runtime files for plink

Language: Vim script - Size: 1000 Bytes - Last synced at: 3 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

hexhead/inbix

In silico research group's bioinformatics toolbox for network and machine learning analysis

Language: C++ - Size: 10.2 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0