naveenluke

tut

bed

ccr

Building the constrained coding regions (CCR) model

colab_ssh

Let Your server connect to colab

devcontainers-rstudio

Zero-setup R with GitHub Codespaces

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

GATK

Germline Variant Calling Nextflow Pipeline Based On GATK4 Best Practices

gitpod_docker_rstudio

No content repository, used to launch RStudio Server in a docker for bioinformatics analyses

Gitpod_R_workspace

intro-to-github

This is a demo repository to practice using GitHub.

JARVIS

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes

motifbreaker

naveenluke.github.io

NGSCheckMate

Software program for checking sample matching for NGS data

NGSCheckMate-nf

Nextflow pipeline to detect matched BAMs with NGSCheckMate

notebooks-base

Base docker image for CellGen JupyterHub

novela-hugo-starter

podman-desktop

Podman Desktop - A graphical tool for developing on containers and Kubernetes

r-codespaces

rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

README-template.md

A README template for anyone to copy and use.

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

scRNA.seq.course

Analysis of single cell RNA-seq data course

somatic-variant-caller

Somatic variant calling pipeline using Mutect2 adapted from GATK Best Practices

test_jupyter_rstudio

testhugotheme

teszt

variant-annotation-comparison-2017

Work supporting the comparison of SnpEff and VEP effect prediction and HGVS identifiers

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

workbench