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ScaleBio Universal ATAC: Citations

Workflow creation

  • 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

  • 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.

  • Bowtie 2

    Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

  • Cutadapt

    Martin M. Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads. EMBnet Journal. 2011

  • FastQC

    Bioinformatics B. FastQC: a quality control tool for high throughput sequence data. Cambridge, UK: Babraham Institute. 2011.

  • MACS3

    Zhang, Yong, et al. "Model-based analysis of ChIP-Seq (MACS)." Genome biology. 2008, 9.9:1-9.

  • Samtools

    Li H, Handsaker B, Wysoker A el al., The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943; PMCID: PMC2723002.

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.

  • Docker

  • Singularity

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

Python Packages

  • Datapane

  • Matplotlib

    J. D. Hunter, (2007). "Matplotlib: A 2D Graphics Environment", Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95.

  • Numpy

    Harris, C. R., et al., (2020). Array programming with NumPy. Nature, 585, 357–362.

  • Pandas

    McKinney, W., & others. (2010). Data structures for statistical computing in python. In Proceedings of the 9th Python in Science Conference (Vol. 445, pp. 51–56).

  • Plotly

    Plotly Technologies Inc. (2015). Collaborative data science Publisher: Plotly Technologies Inc.: Montréal, QC.

  • Pybedtools

    Dale RK, Pedersen BS, and Quinlan AR. (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27(24):3423-3424.

  • Seaborn

    Waskom, M. L., (2021). seaborn: statistical data visualization. Journal of Open Source Software, 6(60), 3021

R Packages

  • AnnotationHub

    Martin Morgan and Lori Shepherd (2022). AnnotationHub: Client to access AnnotationHub resources. R package version 3.2.2.

  • ArchR

    Jeffrey Granja and Ryan Corces (2020). ArchR: Analyzing single-cell regulatory chromatin in R.. R package version 1.0.1.

  • argparse

    Trevor L Davis (2021). argparse: Command Line Optional and Positional Argument Parser. R package version 2.1.3.

  • BiocManager

    Martin Morgan (2021). BiocManager: Access the Bioconductor Project Package Repository. R package version 1.30.16.

  • BSGenome

    Hervé Pagès (2021). BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs. R package version 1.62.0.

  • 'dplyr'

    Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2022). dplyr: A Grammar of Data Manipulation. R package version

  • 'GenomicRanges'

    Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8)

  • ggplot2

    H. Wickham. (2016) ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York

  • glue

    Jim Hester and Jennifer Bryan (2022). glue: Interpreted String Literals. R package version 1.6.2.

  • Seurat

    Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4]

  • yaml

    Shawn P Garbett, Jeremy Stephens et al., (2022). yaml: Methods to Convert R Data to YAML and Back. R package version 2.3.5.