Ecosyste.ms: Awesome

https://github.com/laura-budurlean/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.

1000genomes ancestry ancestry-estimation ancestry-inference ethnicity ethnicity-analysis ethnicity-classifier ethnicity-prediction ngs pca principal-component-analysis wgs

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/structural_variant_discovery

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.

bionano optical-genome-mapping optical-mapping structural-variation structural-variation-calling sv-calling wgs whole-genome-sequencing

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/sv-calling-with-speedseq

A workflow for using SpeedSeq to align and call SVs from WGS data

bioinformatics cnv delly freebayes lumpy speedseq structural-variation sv

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/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.

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/snv-annotation-tools

Useful tools for variant annotation

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/drug-discovery-with-python-and-machine-learning

Explore data collection, analysis, and machine learning for drug discovery. Create predictive models, perform EDA, and deploy as web apps.

biochemistry bioinformatics biostatistics biotechnology chemoinformatics computational-biology drug-discovery machine-learning pharmacokinetics pharmacology python qsar-modeling sklearn webapp

Last synced: 18 Jan 2025

https://github.com/laura-budurlean/laura-budurlean

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/rna-seq-analysis-pipeline

A pipeline to analyze and visualize RNA sequencing data. Includes PCA, heatmap, differential gene expression, and enrichment analysis. with DESeq2

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/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.

Last synced: 27 Jan 2025

https://github.com/laura-budurlean/gatk-wgs-pipeline

GATK WGS workflow

bioinformatics gatk gatk-bestpractices illumina ngs snv wgs wholegenomesequencing

Last synced: 27 Jan 2025