nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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xihaoli/STAARpipeline

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

Language: R - Size: 2.2 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 53 - Forks: 17

xihaoli/STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

Language: R - Size: 251 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 26 - Forks: 17

IARCbioinfo/alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

Language: Nextflow - Size: 3.73 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 26 - Forks: 12

OpenOmics/genome-seek

Clinical Whole Genome and Exome Sequencing Pipeline

Language: Python - Size: 952 KB - Last synced at: about 21 hours ago - Pushed at: about 23 hours ago - Stars: 23 - Forks: 10

kstawiski/seq-pipeline

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

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xihaoli/STAARpipelineSummary

An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies generated by STAARpipeline

Language: R - Size: 1.61 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 9 - Forks: 5

luoyuanlab/autism_precision_medicine

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

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alexcoppe/iWhale

:whale: Dockerized WES pipeline for variants identification in mathced tumor-normal samples

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Vicellken/Whole_exome_sequence

Language: Shell - Size: 31.3 KB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 0

li-lab-genetics/staarpipeline-rap

An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP

Language: R - Size: 62.5 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 2

LOVDnl/LOVDplus

LOVD+ -- LOVD for diagnostics: analysis of whole-exome data using LOVD.

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CCBR/Pipeliner 📦

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Language: Python - Size: 20.2 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

esohkevin/ei-ngs

Workflows for whole-genome/exome sequencing data analysis

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li-lab-genetics/MetaSTAARlite

A lightweight R package for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using MetaSTAARlite pipeline

Language: R - Size: 10.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 3

li-lab-genetics/favorannotator-rap

An app for automatically functionally annotating the variants of whole-genome/whole-exome sequencing (WGS/WES) studies and integrating the functional annotations with the genotype data using FAVORannotator in UK Biobank RAP

Language: R - Size: 24.4 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

mehdimerbah/WES

Whole Exome Sequencing end-to-end pipeline. Starting from whole exome fastq files: Data QC, Adapter Trimming, Reference Genome Alignment, SAM/BAM Validation, Data Recalibration and Variant Calling.

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genomicsITER-developers/wdl

WDL-based pipelines

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genepi-freiburg/seqmeta

SeqMeta pipeline

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XiaoqiLuo/whole_exome_squence_snakemake

Size: 90.8 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

tdayris-perso/wes-mapping-bwa-gatk 📦

Map and post-process your bams for SNP calling

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bioinf/weswgs

Language: R - Size: 27.1 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1

labbcb/hpexome

An automated tool for processing whole-exome sequencing data

Language: Python - Size: 41.6 MB - Last synced at: about 1 month ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 5

li-lab-genetics/MetaSTAARlite-Tutorial

The tutorial for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, MetaSTAARlite and MetaSTAARliteSummary

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GeneMAP-Research/genemap-research.github.io

Genetic Medicine of African Populations

Size: 1.65 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

li-lab-genetics/staarpipelinesummary_indvar-rap

An app for summarizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies in UK Biobank RAP

Language: R - Size: 21.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

li-lab-genetics/staarpipelinesummary_varset-rap

An app for summarizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies in UK Biobank RAP

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petermchale/trfermikit

Discover VNTR-associated DELs that are hard to find using Illumina reads

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CarvalhoFilipeL/CarvalhoFilipeL-Mouw_RABC

Analyses and figures related to Mossanen and Carvalho et al Eur Urol 2021 manuscript entitled "Genomic Features of Muscle-Invasive Bladder Cancer Arising After Prostate Radiotherapy"

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bioinf/afpaper

Scripts and data processing notes for Russian exome sequencing AF paper

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IARCbioinfo/CODEX-nf

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX

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esohkevin/esohkevin.github.io

esohinformatics

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JuanCarlosBio/TFM

END OF MASTER'S PROJECT: Valencian International University VIU

Language: Jupyter Notebook - Size: 41.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

anbianchi/IntegratedSNVINDELSandCNV

An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.

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sbresnahan/TexasCancerGenomics

Analysis of paired tumor-normal whole exome sequencing data generated in a pilot open-access study of participants in Texas.

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GeneMAP-Research/projects

Research projects conducted at the GeneMAP Research Center

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sclayton33/bioinformatics

Code and resources for bioinformatics analyses I've done.

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leahkemp/hyperparathyroid_analysis_20221102

Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.

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LedaKatopodi/library-of-cheatsheets

📑 A library of example code -aka cheatsheets- for tools I use or analyses I carry out pretty often. This repo doubles as an easy way to find the code I need without going through all my scripts.

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snewhouse/exomiser-clone

Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0