BEDOPS: high-performance genomic feature operations
By Shane J. Neph, Scott Kuehn, Alex P. Reynolds, E. Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, J. Vierstra, Sean Thomas and 3 more. Bioinform., 2012
938 citations recorded by the source corpus.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7550298e8ac00c8454e66d57e2fbf1d121a613f1
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In Artificial Intelligence
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- Dmitry Meleshko
- Alla L. Lapidus
- Gordon Gremme
- Anton I. Korobeynikov
- Dmitry Antipov
- Andrey D. Prjibelski
- Sascha Steinbiss
- Julio Collado-Vides
Citations in the corpus
- The stress granule transcriptome reveals principles of mRNA accumulation in stress granules (2017, neutral): “4.26 was used performed to convert the gtf file into a bed file, using the command ‘gtf2bed’ (Neph et al., 2012).”
- GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations (2013, methodology): “Besides the mentioned software for processing annotations, there are also some popular command-line software tools available to automatically process annotations given in the BED and GFF format [16], [17].”
- Using SPAdes De Novo Assembler (2020, methodology): “• STAR (Dobin et al., 2013) or Hisat2 (Kim, Langmead, & Salzberg, 2015) aligners • samtools (Li et al., 2009) • bedops (Neph et al., 2012) • RSeQC (Wang, Wang, & Li, 2012) The resulting alignments are required to be sorted (automatically done when using STAR with --outSAMtype BAM SortedByCoordinate…”
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 (2018, methodology): “From the intensity files, macs2 software (7) and BEDOPS (8) commands were run to obtain enrichment regions.”