ArticleGenomics, proteomics & bioinformatics2021
CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis.
Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- ESR1 mutations and CDK4/6 inhibitor choice shape clonal selection and adaptive cell states during acquired resistance.Genome medicine · 2026Article
- Lack of synergy between AR-targeted therapies and PARP inhibitors in homologous recombination-proficient prostate cancer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Epigenetic subtypes of high-grade T1 bladder cancer reveal intra-tumor heterogeneity and distinct interactions with tumor microenvironment.Theranostics · 2026Article
- RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.PloS one · 2026Article
- Requirement for Cyclin D1 Underlies Cell-Autonomous HIF2 Dependence in Kidney Cancer.Cancer discovery · 2025Article
- HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.Cell · 2025Article
- Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.BMC genomics · 2025Article
- UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.BMC bioinformatics · 2025Article
- ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer.Cell reports · 2024Article
- Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts.Nature communications · 2024Article
- Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma.Cell reports · 2024Article
- Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer.Molecular cancer therapeutics · 2024Article
- Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Churros: a Docker-based pipeline for large-scale epigenomic analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases.Nature biotechnology · 2024Article
- Heterogeneity and transcriptional drivers of triple-negative breast cancer.Cell reports · 2023Article
- Combination Therapies to Improve the Efficacy of Immunotherapy in Triple-negative Breast Cancer.Molecular cancer therapeutics · 2023Article
- Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer.Cancer research · 2023Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference database, and pathway analysis. CoBRA is publicly available online at https://bitbucket.org/cfce/cobra.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.