Laura Budurlean's repositories
PCA-Ethnicity-Determination-from-WGS-Data
A pipeline utilizing PCA on 1000 genomes and WGS data from your own samples to determine or validate ancestry of an individual.
SNV-Annotation-Tools
Useful tools for variant annotation
SV-calling-with-SpeedSeq
A workflow for using SpeedSeq to align and call SVs from WGS data
Differentially-mutated-genes
Fisher's tests (with or without) correction for multiple testing on 2x2 contingency tables. Uses a list of genes from two populations to test if any are significantly mutated/disrupted by SVs in one population vs another. Specifically set up to test for SVs affecting genes.
GATK-WGS-Pipeline
GATK WGS workflow
maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
RNA-Seq-Analysis-Pipeline
A pipeline to analyze and visualize RNA sequencing data. Includes PCA, heatmap, differential gene expression, and enrichment analysis. with DESeq2
Structural-Variant-Detection-Annotation-and-Plotting-Tools
Useful tools for the analysis of structural variation (SV) in the genome. Includes tools used for SV detection, annotation, and plotting resources.
structural_variant_OGM_WGS_pipeline
A combination of optical genome mapping with Bionano and whole genome sequencing short-read data. This pipeline was created to help integrate structural variant calling from these two technologies.