Salmon provides fast and bias-aware quantification of transcript expression R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford Nature methods 14 (4), 417-419, 2017 | 8535 | 2017 |
Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 843 | 2018 |
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms R Patro, SM Mount, C Kingsford Nature biotechnology 32 (5), 462-464, 2014 | 775 | 2014 |
TransRate: reference-free quality assessment of de novo transcriptome assemblies R Smith-Unna, C Boursnell, R Patro, JM Hibberd, S Kelly Genome research 26 (8), 1134-1144, 2016 | 744 | 2016 |
Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023 | 263 | 2023 |
Global network alignment using multiscale spectral signatures R Patro, C Kingsford Bioinformatics 28 (23), 3105-3114, 2012 | 251 | 2012 |
Identification of alternative topological domains in chromatin D Filippova, R Patro, G Duggal, C Kingsford Algorithms for Molecular Biology 9, 1-11, 2014 | 247 | 2014 |
Tximeta: Reference sequence checksums for provenance identification in RNA-seq MI Love, C Soneson, PF Hickey, LK Johnson, NT Pierce, L Shepherd, ... PLoS computational biology 16 (2), e1007664, 2020 | 203 | 2020 |
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data A Srivastava, L Malik, T Smith, I Sudbery, R Patro Genome biology 20, 1-16, 2019 | 199 | 2019 |
A general-purpose counting filter: Making every bit count P Pandey, MA Bender, R Johnson, R Patro Proceedings of the 2017 ACM international conference on Management of Data …, 2017 | 188 | 2017 |
RNA sequencing data: hitchhiker's guide to expression analysis K Van den Berge, KM Hembach, C Soneson, S Tiberi, L Clement, MI Love, ... Annual Review of Biomedical Data Science 2, 139-173, 2019 | 139 | 2019 |
Alignment and mapping methodology influence transcript abundance estimation A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ... Genome biology 21, 1-29, 2020 | 138 | 2020 |
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes A Srivastava, H Sarkar, N Gupta, R Patro Bioinformatics 32 (12), i192-i200, 2016 | 133 | 2016 |
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification MI Love, C Soneson, R Patro F1000Research 7, 2018 | 127 | 2018 |
Mantis: a fast, small, and exact large-scale sequence-search index P Pandey, F Almodaresi, MA Bender, M Ferdman, R Johnson, R Patro Cell systems 7 (2), 201-207. e4, 2018 | 113 | 2018 |
Squeakr: an exact and approximate k-mer counting system P Pandey, MA Bender, R Johnson, R Patro Bioinformatics 34 (4), 568-575, 2018 | 102 | 2018 |
Maximum likelihood estimation of biological relatedness from low coverage sequencing data M Lipatov, K Sanjeev, R Patro, KR Veeramah BioRxiv, 023374, 2015 | 92 | 2015 |
Nonparametric expression analysis using inferential replicate counts A Zhu, A Srivastava, JG Ibrahim, R Patro, MI Love Nucleic Acids Research 47 (18), e105-e105, 2019 | 82 | 2019 |
A space and time-efficient index for the compacted colored de Bruijn graph F Almodaresi, H Sarkar, A Srivastava, R Patro Bioinformatics 34 (13), i169-i177, 2018 | 82 | 2018 |
Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford BioRxiv, 021592, 2015 | 77 | 2015 |