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Author: Rob Patro

Rankings

  • All-time downloads: 82,026 (rank: 1,914 )
  • Categories:
    • bioinformatics: 77,920 (rank: 13 )
    • cancer biology: 1,048 (rank: 8,859 (tie) )
    • genetics: 3,058 (rank: 6,377 (tie) )

Downloads per author, site-wide

Preprints

Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

bioinformatics more details view paper
  • Downloaded 24,430 times
  • Download rankings, all-time:
    • Site-wide: 319
    • In bioinformatics: 5
  • Year to date:
    • Site-wide: 6,582
  • Since beginning of last month:
    • Site-wide: 5,953

RapMap: A Rapid, Sensitive and Accurate Tool for Mapping RNA-seq Reads to Transcriptomes

bioinformatics more details view paper
  • Downloaded 14,941 times
  • Download rankings, all-time:
    • Site-wide: 557
    • In bioinformatics: 18
  • Year to date:
    • Site-wide: 37,865
  • Since beginning of last month:
    • Site-wide: 54,199

Bioconda: A sustainable and comprehensive software distribution for the life sciences

bioinformatics more details view paper
  • Downloaded 6,123 times
  • Download rankings, all-time:
    • Site-wide: 1,805
    • In bioinformatics: 120
  • Year to date:
    • Site-wide: 9,495
  • Since beginning of last month:
    • Site-wide: 21,667

Alignment and mapping methodology influence transcript abundance estimation

bioinformatics more details view paper
  • Downloaded 5,609 times
  • Download rankings, all-time:
    • Site-wide: 2,031
    • In bioinformatics: 150
  • Year to date:
    • Site-wide: 5,234
  • Since beginning of last month:
    • Site-wide: 56,376

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

bioinformatics more details view paper
  • Downloaded 3,526 times
  • Download rankings, all-time:
    • Site-wide: 3,882
    • In bioinformatics: 368
  • Year to date:
    • Site-wide: 3,121
  • Since beginning of last month:
    • Site-wide: 31,469

Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data

genetics more details view paper
  • Downloaded 3,058 times
  • Download rankings, all-time:
    • Site-wide: 4,737
    • In genetics: 189
  • Year to date:
    • Site-wide: 14,229
  • Since beginning of last month:
    • Site-wide: 14,757

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

bioinformatics more details view paper
  • Downloaded 2,811 times
  • Download rankings, all-time:
    • Site-wide: 5,349
    • In bioinformatics: 541
  • Year to date:
    • Site-wide: 40,678
  • Since beginning of last month:
    • Site-wide: 32,285

Mantis: A Fast, Small, and Exact Large-Scale Sequence Search Index

bioinformatics more details view paper
  • Downloaded 2,792 times
  • Download rankings, all-time:
    • Site-wide: 5,406
    • In bioinformatics: 551
  • Year to date:
    • Site-wide: 60,506
  • Since beginning of last month:
    • Site-wide: 53,838

Squeakr: An Exact and Approximate k-mer Counting System

bioinformatics more details view paper
  • Downloaded 1,841 times
  • Download rankings, all-time:
    • Site-wide: 9,961
    • In bioinformatics: 1,152
  • Year to date:
    • Site-wide: 56,897
  • Since beginning of last month:
    • Site-wide: None

Nonparametric expression analysis using inferential replicate counts

bioinformatics more details view paper
  • Downloaded 1,645 times
  • Download rankings, all-time:
    • Site-wide: 11,796
    • In bioinformatics: 1,369
  • Year to date:
    • Site-wide: 76,064
  • Since beginning of last month:
    • Site-wide: 78,117

Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification

bioinformatics more details view paper
  • Downloaded 1,524 times
  • Download rankings, all-time:
    • Site-wide: 13,100
    • In bioinformatics: 1,502
  • Year to date:
    • Site-wide: 70,263
  • Since beginning of last month:
    • Site-wide: 61,346

Rainbowfish: A Succinct Colored de Bruijn Graph Representation

bioinformatics more details view paper
  • Downloaded 1,224 times
  • Download rankings, all-time:
    • Site-wide: 18,311
    • In bioinformatics: 2,102
  • Year to date:
    • Site-wide: 142,177
  • Since beginning of last month:
    • Site-wide: None

CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

cancer biology more details view paper
  • Downloaded 1,048 times
  • Download rankings, all-time:
    • Site-wide: 23,022
    • In cancer biology: 556
  • Year to date:
    • Site-wide: 17,737
  • Since beginning of last month:
    • Site-wide: 88,811

Rich chromatin structure prediction from Hi-C data

bioinformatics more details view paper
  • Downloaded 1,046 times
  • Download rankings, all-time:
    • Site-wide: 23,098
    • In bioinformatics: 2,642
  • Year to date:
    • Site-wide: 121,015
  • Since beginning of last month:
    • Site-wide: 105,911

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

bioinformatics more details view paper
  • Downloaded 1,017 times
  • Download rankings, all-time:
    • Site-wide: 24,019
    • In bioinformatics: 2,739
  • Year to date:
    • Site-wide: 78,660
  • Since beginning of last month:
    • Site-wide: 113,934

A space and time-efficient index for the compacted colored de Bruijn graph

bioinformatics more details view paper
  • Downloaded 1,005 times
  • Download rankings, all-time:
    • Site-wide: 24,442
    • In bioinformatics: 2,785
  • Year to date:
    • Site-wide: 92,112
  • Since beginning of last month:
    • Site-wide: None

Graph regularized, semi-supervised learning improves annotation of de novo transcriptomes

bioinformatics more details view paper
  • Downloaded 987 times
  • Download rankings, all-time:
    • Site-wide: 25,124
    • In bioinformatics: 2,847
  • Year to date:
    • Site-wide: 143,383
  • Since beginning of last month:
    • Site-wide: None

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections

bioinformatics more details view paper
  • Downloaded 924 times
  • Download rankings, all-time:
    • Site-wide: 27,627
    • In bioinformatics: 3,126
  • Year to date:
    • Site-wide: 9,789
  • Since beginning of last month:
    • Site-wide: 86,894

Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index

bioinformatics more details view paper
  • Downloaded 838 times
  • Download rankings, all-time:
    • Site-wide: 31,651
    • In bioinformatics: 3,521
  • Year to date:
    • Site-wide: 34,116
  • Since beginning of last month:
    • Site-wide: 88,726

Tximeta: reference sequence checksums for provenance identification in RNA-seq

bioinformatics more details view paper
  • Downloaded 734 times
  • Download rankings, all-time:
    • Site-wide: 38,138
    • In bioinformatics: 4,110
  • Year to date:
    • Site-wide: 87,862
  • Since beginning of last month:
    • Site-wide: 125,326

Compression of short-read sequences using path encoding

bioinformatics more details view paper
  • Downloaded 725 times
  • Download rankings, all-time:
    • Site-wide: 38,774
    • In bioinformatics: 4,171
  • Year to date:
    • Site-wide: 137,367
  • Since beginning of last month:
    • Site-wide: 45,531

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

bioinformatics more details view paper
  • Downloaded 708 times
  • Download rankings, all-time:
    • Site-wide: 40,062
    • In bioinformatics: 4,304
  • Year to date:
    • Site-wide: 122,896
  • Since beginning of last month:
    • Site-wide: 108,881

Compression of quantification uncertainty for scRNA-seq counts

bioinformatics more details view paper
  • Downloaded 698 times
  • Download rankings, all-time:
    • Site-wide: 40,798
    • In bioinformatics: 4,360
  • Year to date:
    • Site-wide: 64,912
  • Since beginning of last month:
    • Site-wide: 95,868

Quark enables semi-reference-based compression of RNA-seq data

bioinformatics more details view paper
  • Downloaded 681 times
  • Download rankings, all-time:
    • Site-wide: 42,120
    • In bioinformatics: 4,488
  • Year to date:
    • Site-wide: 138,995
  • Since beginning of last month:
    • Site-wide: None

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

bioinformatics more details view paper
  • Downloaded 621 times
  • Download rankings, all-time:
    • Site-wide: 47,451
    • In bioinformatics: 4,930
  • Year to date:
    • Site-wide: 110,684
  • Since beginning of last month:
    • Site-wide: 111,095

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

bioinformatics more details view paper
  • Downloaded 391 times
  • Download rankings, all-time:
    • Site-wide: 79,437
    • In bioinformatics: 7,291
  • Year to date:
    • Site-wide: 125,607
  • Since beginning of last month:
    • Site-wide: 93,050

A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing

bioinformatics more details view paper
  • Downloaded 329 times
  • Download rankings, all-time:
    • Site-wide: 91,975
    • In bioinformatics: 8,104
  • Year to date:
    • Site-wide: 16,281
  • Since beginning of last month:
    • Site-wide: 84,502

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data

bioinformatics more details view paper
  • Downloaded 272 times
  • Download rankings, all-time:
    • Site-wide: 105,103
    • In bioinformatics: 8,922
  • Year to date:
    • Site-wide: 21,207
  • Since beginning of last month:
    • Site-wide: 26,999

Accounting for fragments of unexpectedorigin improves transcript quantification inRNA-seq simulations focused on increased realism

bioinformatics more details view paper
  • Downloaded 269 times
  • Download rankings, all-time:
    • Site-wide: 105,861
    • In bioinformatics: 8,960
  • Year to date:
    • Site-wide: 21,485
  • Since beginning of last month:
    • Site-wide: 10,317

An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees

bioinformatics more details view paper
  • Downloaded 209 times
  • Download rankings, all-time:
    • Site-wide: 120,730
    • In bioinformatics: 9,811
  • Year to date:
    • Site-wide: 29,862
  • Since beginning of last month:
    • Site-wide: 101,840

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