The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Bioconda: sustainable and comprehensive software distribution for the life sciences
Open accessPublished version of a preprint
Abstract
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Salmon provides fast and bias-aware quantification of transcript expression
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700
Self-citationNear-optimal probabilistic RNA-seq quantification
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology · doi:10.1038/nbt.3519 · Cited by 9,723
1,500 scientists lift the lid on reproducibility
Baker, M. (2016) · Nature · doi:10.1038/533452a · Cited by 4,209
A manifesto for reproducible science
Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017) · Nature Human Behaviour · doi:10.1038/s41562-016-0021 · Cited by 3,397
Singularity: Scientific containers for mobility of compute
Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017) · PLOS ONE · doi:10.1371/journal.pone.0177459 · Cited by 2,740
Research works printed but not linked: 4
- Mesirov, J. P. Science 327, 415–416 (2010). · DOI · Paper page
- Afgan, E. et al. Nucleic Acids Res. 44, W3–W10 (2016). · DOI
- Köster, J. & Rahmann, S. Bioinformatics 28, 2520–2522 (2012). · DOI · Paper page
- Field, D. et al. Nat. Biotechnol. 24, 801–803 (2006). · DOI
Cited by
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187
NanoPack: visualizing and processing long-read sequencing data
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Uritskiy, G. V., DiRuggiero, J., & Taylor, J. (2018) · Microbiome · doi:10.1186/s40168-018-0541-1 · Cited by 2,642
Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp
Chen, S. (2023) · iMeta · doi:10.1002/imt2.107 · Cited by 2,166
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Berhanu Lemma, R., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Manosalva Pérez, N., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1113 · Cited by 1,935
Metadata
- Authors
- The Bioconda Team, Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., & Köster, J.
- Venue
- Nature Methods
- Published
- 2018-07
- Volume
- 15
- Issue
- 7
- Pages
- 475-476
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2765745983
- Cited by
- 1,641
- References
- 6
- FWCI
- 164.40
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.springer.com/tdm (tdm)
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