Pinned Repositories
2014-streaming
2015-metagenome-assembly
Makefile pipeline for metagenome assembly.
AssociationAnalysis
Rare variants association analysis tests is not only burden test. There are lots of test we can use.
ATAC-Seq
Snakemake pipeline for ATAC-Seq
Bisulfite
BulkRNASeq
Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.
gatkVariantCalling
Snakemake pipeline for variant calling using GATK
miRNA
Snakemake pipeline to detect miRNA
SomaticMutations
This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)
StructureVariations
Snakemake pipeline for detecting, annotating, filtering and visualising structure variations and gene fusions from WGS/WES.
SherineAwad's Repositories
SherineAwad/gatkVariantCalling
Snakemake pipeline for variant calling using GATK
SherineAwad/SomaticMutations
This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2)
SherineAwad/StructureVariations
Snakemake pipeline for detecting, annotating, filtering and visualising structure variations and gene fusions from WGS/WES.
SherineAwad/miRNA
Snakemake pipeline to detect miRNA
SherineAwad/AssociationAnalysis
Rare variants association analysis tests is not only burden test. There are lots of test we can use.
SherineAwad/ATAC-Seq
Snakemake pipeline for ATAC-Seq
SherineAwad/Bisulfite
SherineAwad/BulkRNASeq
Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.
SherineAwad/ConePhotoreceptors
SherineAwad/cutandtag
SherineAwad/demultiplex
SherineAwad/Downsampling
Different strategies for Downsampling: Downsampling is not just throwing a read
SherineAwad/gala
Galactic and gravitational dynamics in Python
SherineAwad/IsoformSwitches
SherineAwad/Kinship
Quick analysis for kinship, relatedness, IBS, IBD
SherineAwad/LigandReceptorsInteractions
SherineAwad/lncRNA
Snakemake pipeline to detect novel lncRNA
SherineAwad/magnifier
Troubleshooting Pipeline: Investigates samples for any possible issue
SherineAwad/miscellaneous
Random scripts
SherineAwad/MouseAgingRetina
SherineAwad/Neurogenesis_zebrafish
SherineAwad/OCT4scRNA-ATAC
SherineAwad/Retina_AMD
SherineAwad/Ribofilio
Ribofilio is a python tool to estimate ribosomes drop off rate.
SherineAwad/RNASeqFusion
SherineAwad/RNASeqVariantCalling
GATK variant calling for RNASeq
SherineAwad/scATAC
SherineAwad/StemCell_Composition
Inferring stem cell composition using variant calling
SherineAwad/VC_Benchmark
A part of benchmark project to compare Snakemake vs Streamflow: GATK variant calling pipeline is used for the benchmarking study.
SherineAwad/VQSR
GATK Variant Quality Score Recalibration for filtering variant calling set