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nf-core/hicar: Citations

HiC on Accessible Regulatory DNA (HiCAR)

Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Mol Cell. 2022 Mar 17;82(6):1225-1238.e6. doi: 10.1016/j.molcel.2022.01.023. Epub 2022 Feb 22. PMID: 35196517; PMCID: PMC8934281.

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

  • BWA

    Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234.

  • BEDTools

    Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

  • ChIPpeakAnno

    Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237. PMID: 20459804; PMCID: PMC3098059.

  • clusterProfiler

    Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28. PMID: 22455463; PMCID: PMC3339379.

  • circos

    Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009 Sep;19(9):1639-45. doi: 10.1101/gr.092759.109. Epub 2009 Jun 18. PMID: 19541911; PMCID: PMC2752132.

  • cooler

    Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020 Jan 1;36(1):311-316. doi: 10.1093/bioinformatics/btz540. PMID: 31290943.

  • cooltools

  • diffhic

    Lun AT, Smyth GK. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics. 2015 Aug 19;16:258. doi: 10.1186/s12859-015-0683-0. PMID: 26283514; PMCID: PMC4539688.

  • edgeR

    Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. PMID: 19910308; PMCID: PMC2796818.

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

  • GenMap

    Pockrandt C, Alzamel M, Iliopoulos CS, Reinert K. GenMap: ultra-fast computation of genome mappability. Bioinformatics. 2020 Jun 1;36(12):3687-3692. doi: 10.1093/bioinformatics/btaa222. PMID: 32246826; PMCID: PMC7320602.

  • HiC-DC+

    Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS. HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Nat Commun. 2021 Jun 7;12(1):3366. doi: 10.1038/s41467-021-23749-x. PMID: 34099725; PMCID: PMC8184932.

  • HiCExplorer

    Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w. PMID: 29335486; PMCID: PMC5768762.

  • Homer

    Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

  • igv.js

    Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013 Mar;14(2):178-92. doi: 10.1093/bib/bbs017. Epub 2012 Apr 19. PMID: 22517427; PMCID: PMC3603213.

  • Juicer_tools

    Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016 Jul;3(1):95-8. doi: 10.1016/j.cels.2016.07.002. PMID: 27467249; PMCID: PMC5846465.

  • MACS2

    Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715.

  • MAPS

    Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol. 2019 Apr 15;15(4):e1006982. doi: 10.1371/journal.pcbi.1006982. PMID: 30986246; PMCID: PMC6483256.

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

  • pairsqc

  • pairtools

  • peakachu

    Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F. A supervised learning framework for chromatin loop detection in genome-wide contact maps. Nat Commun. 2020 Jul 9;11(1):3428. doi: 10.1038/s41467-020-17239-9. PMID: 32647330; PMCID: PMC7347923.

  • SAMtools

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

  • trackViewer

    Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods. 2019 Jun;16(6):453-454. doi: 10.1038/s41592-019-0430-y. PMID: 31133757.

  • UCSC tools

    Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.