marianakhoul Goto Github PK

asgard-scrna-seq-drug-repurposing

Building the Asgard scRNA-seq pipeline to run on HPC SLURM.

azure

Personal repository that contains requirements for Azure certification courses and code to run services. Main content from Microsoft Azure official documentation pages and Udemy AZ-204 Developing for Microsoft Azure Exam Prep Course by Scott Duffy https://www.udemy.com/share/101Ywk3@pZmggxxkKkQ7TegAzDlyuqd8gWvS2sfHZLlJvf0r7IxnxhTexzLGx0X-xOrVrkU9qQ==/

bash-commands

Repository to store some shortcut bash commands

bmi706-visualization-project

crpc-sv-pattern-study

docker

Repository to hold my Docker commands, examples and Dockerfiles for future need

gatk

Notes I took about the GATK pipeline from the Broad Institute Documentations https://gatk.broadinstitute.org/hc/en-us

gatk4-genome-processing-pipeline-azure

Workflows used for processing whole genome sequence data + germline variant calling. Edited paths to work on my own data and data storage locations.

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

marianakhoul.github.io

mutect2_snakemake

padog

Pathway Analysis with Down-weighting of Overlapping Genes

purecn

snakemake

Personal repository to store syntax, examples and notes for Snakemake collected from different resources

sra-toolkit

How to download SRA toolkit and commands to download data

statistics-in-r

submitting-jobs-to-job-scheduler

Repository for storing commands and scripts for using SLURM and QSUB as job schedulers

sv_10x_analysis

Structural variation analysis of 10X Genomics linked-read data

titancna_10x_snakemake

Snakemake workflow for 10X Genomics WGS analysis using TitanCNA - GavinHaLab Forked Repo. Fixed the Issue I was getting from the original repo: Error: RangedData objects are deprecated and the coercion method from data.frame or DataTable to RangedData is now defunct. Please migrate your code to use GRanges or GRangesList objects instead.

vcf2maf

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

wdl

Personal repository to store syntax, examples and notes for WDL collected from different resources