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Citations.txt
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Citations.txt
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Nextflow:
Di Tommaso, Paolo, et al. "Nextflow enables reproducible computational workflows." Nature biotechnology 35.4 (2017): 316-319.
Bioconda:
Grüning, Björn, et al. "Bioconda: sustainable and comprehensive software distribution for the life sciences." Nature methods 15.7 (2018): 475-476.
CUTRUNTools:
Zhu, Qian, et al. "CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis." Genome biology 20.1 (2019): 192.
SEACR:
Meers, Michael P., Dan Tenenbaum, and Steven Henikoff. "Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling." Epigenetics & chromatin 12.1 (2019): 42.
R:
R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
BioContainers:
Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I Nesvizhskii, Yasset Perez-Riverol, BioContainers: an open-source and community-driven framework for software standardization, Bioinformatics, Volume 33, Issue 16, 15 August 2017, Pages 2580–2582, https://doi.org/10.1093/bioinformatics/btx192
Bowtie2:
Langmead, Ben, and Steven L. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature methods 9.4 (2012): 357.
faCount:
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.
Samtools:
Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
FastQC:
Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trimmomatic:
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.
bedtools:
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
bedGraphToBigWig:
BigWig and BigBed tools: Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7.
MACS2:
Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137