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A Snakemake pipeline for Quality Control of Whole Genome Sequencing data
Tools for processing and analyzing structural variants.
Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data.
Example notebooks of pyCircos
code for figure 2 of the cancer/copy number project for BIO 465
Subset of scripts created during the CSHL URP 2018. Developing method to extract predictive biomarkers from PDAC patient derived organoids. Using COREs from CNV and WES data from pancreatic tumor o…
Helped a grad student in my lab with a data processing problem he had regarding CNV genotyping calls for 4444 CNVs spread across 96 samples.
Each significant copy number variation(CNV) in the human genome is related to a specific disease. So, in this project the aim to detect significant CNV using machine learning.
Long read based human genomic structural variation detection with cuteSV
Pipeline for de novo clustering of long transcriptomic reads
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
Run Circos software in a Jupyter environment served by MyBinder.org.
Identifying fusion transcripts using paired-end RNA-seq
A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.