Genome-wide extraction of real-valued signals hidden in noisy multisample HTS data
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Jul 6, 2026 - Python
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cut-and-run
Here are 6 public repositories matching this topic...
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
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Sep 8, 2023 - Python
Personal portfolio of Dr. Mallikarjuna Thippana — computational biologist specializing in genomics & epigenomics (bulk RNA-seq, ChIP-seq, ATAC-seq, CUT&RUN), single-cell & spatial multi-omics, and statistical ML for biological data.
github-pages portfolio data-science bioinformatics rna-seq personal-website computational-biology cancer-genomics chip-seq atac-seq single-cell-genomics epigenomics spatial-transcriptomics cut-and-run phd-portfolio
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Jul 4, 2026 - HTML
qPCR Plate Planner is a browser-based tool to streamline the design, execution, and analysis of qPCR experiments. To have the AI functionality visit https://huggingface.co/spaces/mahmood-iab/qPCR-Plate-Planner-AI
epigenetics workflow-automation experimental-design qpcr-analysis gene-quantification master-mix plate-layout-design cut-and-run workflow-automation-tools fold-change-analysis chip-qpcr 384-well ddct-analysis chromatin-enrichment
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May 12, 2026 - HTML
Self-hosted CUT&RUN bioinformatics platform for the Ferguson Lab at UCSD. Replicates CUTANA Cloud and extends it with trimming, SEACR/MACS2, DiffBind, custom heatmaps, Pearson correlation, & Roman normalization. React + FastAPI + PostgreSQL on EC2.
react bioinformatics pipeline genomics postgresql igv chromatin epigenomics peak-calling fastapi diffbind cut-and-run
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Jul 11, 2026 - Python
A modular, production-ready Snakemake pipeline for CUT&RUN epigenomic analysis — featuring E. coli spike-in normalization, SEACR peak calling, fragment size analysis, and comprehensive QC reporting. Designed following ENCODE and nf-core best practices.
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Jul 15, 2026 - Python
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