Brent S. Pedersen

18 papers Journal 18
YearRankTypeTitle / Venue / Authors
2025 J jnl
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs.
Bioinform.
Brent S. Pedersen, Aaron R. Quinlan
2022 J jnl
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.
PLoS Comput. Biol.
Erik Garrison, Zev N. Kronenberg, Eric T. Dawson, Brent S. Pedersen, Pjotr Prins
2022 J jnl
Author Correction: Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools.
Nat. Comput. Sci.
Hao Hou, Brent S. Pedersen, Aaron R. Quinlan
2022 J jnl
Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.
BMC Bioinform.
Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir, Aaron R. Quinlan
2021 J jnl
Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools.
Nat. Comput. Sci.
Hao Hou, Brent S. Pedersen, Aaron R. Quinlan
2021 J jnl
Unfazed: parent-of-origin detection for large and small de novo variants.
Bioinform.
Jonathan R. Belyeu, Thomas A. Sasani, Brent S. Pedersen, Aaron R. Quinlan
2018 J jnl
Mosdepth: quick coverage calculation for genomes and exomes.
Bioinform.
Brent S. Pedersen, Aaron R. Quinlan
2018 J jnl
hts-nim: scripting high-performance genomic analyses.
Bioinform.
Brent S. Pedersen, Aaron R. Quinlan
2017 J jnl
bíogo/hts: high throughput sequence handling for the Go language.
J. Open Source Softw.
R. Daniel Kortschak, Brent S. Pedersen, David L. Adelson
2017 J jnl
cyvcf2: fast, flexible variant analysis with Python.
Bioinform.
Brent S. Pedersen, Aaron R. Quinlan
2015 J jnl
Efficient "pythonic" access to FASTA files using pyfaidx.
PeerJ Prepr.
Matthew D. Shirley, Zhaorong Ma, Brent S. Pedersen, Sarah J. Wheelan
2014 J jnl
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.
Briefings Bioinform.
Subhajyoti De, Brent S. Pedersen, Katerina J. Kechris
2013 J jnl
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.
Bioinform.
Brent S. Pedersen, Ivana V. Yang, Subhajyoti De
2012 J jnl
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated
Bioinform.
Brent S. Pedersen, David A. Schwartz, Ivana V. Yang, Katerina J. Kechris
2011 J jnl
BioStar: An Online Question & Answer Resource for the Bioinformatics Community.
PLoS Comput. Biol.
Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, István Albert
2011 J jnl
Gobe: an interactive, web-based tool for comparative genomic visualization.
Bioinform.
Brent S. Pedersen, Haibao Tang, Michael Freeling
2011 J jnl
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.
Bioinform.
Ryan K. Dale, Brent S. Pedersen, Aaron R. Quinlan
2011 J jnl
Screening synteny blocks in pairwise genome comparisons through integer programming.
BMC Bioinform.
Haibao Tang, Eric Lyons, Brent S. Pedersen, James C. Schnable, Andrew H. Paterson, Michael Freeling