Author: Michael Isaiah Love

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Preprints

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

• Downloaded 25,191 times
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  • Site-wide: 442
  • In bioinformatics: 6
• Year to date:
  • Site-wide: 6,946
• Since beginning of last month:
  • Site-wide: 18,281

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

• Downloaded 23,865 times
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  • Site-wide: 469
  • In bioinformatics: 9
• Year to date:
  • Site-wide: 1,942
• Since beginning of last month:
  • Site-wide: 1,722

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

• Downloaded 7,342 times
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  • Site-wide: 2,066
  • In genomics: 153
• Year to date:
  • Site-wide: 4,199
• Since beginning of last month:
  • Site-wide: 1,198

Alignment and mapping methodology influence transcript abundance estimation

• Downloaded 6,462 times
• Download rankings, all-time:
  • Site-wide: 2,464
  • In bioinformatics: 160
• Year to date:
  • Site-wide: 65,329
• Since beginning of last month:
  • Site-wide: 14,925

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

• Downloaded 4,869 times
• Download rankings, all-time:
  • Site-wide: 3,627
  • In bioinformatics: 286
• Year to date:
  • Site-wide: 41,899
• Since beginning of last month:
  • Site-wide: 89,400

An approach for normalization and quality control for NanoString RNA expression data

• Downloaded 3,159 times
• Download rankings, all-time:
  • Site-wide: 6,801
  • In genomics: 643
• Year to date:
  • Site-wide: 5,434
• Since beginning of last month:
  • Site-wide: 10,405

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

• Downloaded 3,098 times
• Download rankings, all-time:
  • Site-wide: 6,981
  • In bioinformatics: 644
• Year to date:
  • Site-wide: 74,694
• Since beginning of last month:
  • Site-wide: 116,363

Flexible expressed region analysis for RNA-seq with derfinder

• Downloaded 2,580 times
• Download rankings, all-time:
  • Site-wide: 9,121
  • In bioinformatics: 951
• Year to date:
  • Site-wide: 42,048
• Since beginning of last month:
  • Site-wide: 142,041

zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications

• Downloaded 2,390 times
• Download rankings, all-time:
  • Site-wide: 10,256
  • In bioinformatics: 1,091
• Year to date:
  • Site-wide: 64,630
• Since beginning of last month:
  • Site-wide: 119,754

Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

• Downloaded 1,937 times
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  • Site-wide: 14,116
  • In genetics: 559
• Year to date:
  • Site-wide: 46,278
• Since beginning of last month:
  • Site-wide: 160,776

Plotgardener: Cultivating precise multi-panel figures in R

• Downloaded 1,909 times
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  • Site-wide: 14,418
  • In bioinformatics: 1,559
• Year to date:
  • Site-wide: 54,395
• Since beginning of last month:
  • Site-wide: 17,686

Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development

• Downloaded 1,873 times
• Download rankings, all-time:
  • Site-wide: 14,861
  • In genomics: 1,332
• Year to date:
  • Site-wide: 171,246
• Since beginning of last month:
  • Site-wide: 148,066

Comparative analysis of neutrophil and monocyte epigenomes

• Downloaded 1,827 times
• Download rankings, all-time:
  • Site-wide: 15,454
  • In genomics: 1,394
• Year to date:
  • Site-wide: 122,057
• Since beginning of last month:
  • Site-wide: 90,023

Nonparametric expression analysis using inferential replicate counts

• Downloaded 1,810 times
• Download rankings, all-time:
  • Site-wide: 15,683
  • In bioinformatics: 1,699
• Year to date:
  • Site-wide: 140,510
• Since beginning of last month:
  • Site-wide: 91,008

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

• Downloaded 1,796 times
• Download rankings, all-time:
  • Site-wide: 15,873
  • In bioinformatics: 1,746
• Year to date:
  • Site-wide: 74,603
• Since beginning of last month:
  • Site-wide: 91,256

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

• Downloaded 1,416 times
• Download rankings, all-time:
  • Site-wide: 23,130
  • In genomics: 2,031
• Year to date:
  • Site-wide: 44,915
• Since beginning of last month:
  • Site-wide: 25,732

Genetic influences on cell type specific gene expression and splicing during neurogenesis elucidate regulatory mechanisms of brain traits

• Downloaded 1,322 times
• Download rankings, all-time:
  • Site-wide: 25,812
  • In genetics: 1,042
• Year to date:
  • Site-wide: 29,792
• Since beginning of last month:
  • Site-wide: 76,949

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

• Downloaded 1,167 times
• Download rankings, all-time:
  • Site-wide: 31,429
  • In genetics: 1,263
• Year to date:
  • Site-wide: 48,353
• Since beginning of last month:
  • Site-wide: 78,455

MOVIE: Multi-Omics VIsualization of Estimated contributions

• Downloaded 1,130 times
• Download rankings, all-time:
  • Site-wide: 33,054
  • In bioinformatics: 3,489
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 147,308

Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications

• Downloaded 1,115 times
• Download rankings, all-time:
  • Site-wide: 33,749
  • In bioinformatics: 3,585
• Year to date:
  • Site-wide: 99,251
• Since beginning of last month:
  • Site-wide: 145,997

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity

• Downloaded 965 times
• Download rankings, all-time:
  • Site-wide: 42,134
  • In bioinformatics: 4,348
• Year to date:
  • Site-wide: 164,214
• Since beginning of last month:
  • Site-wide: 65,570

matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling

• Downloaded 870 times
• Download rankings, all-time:
  • Site-wide: 49,517
  • In bioinformatics: 5,096
• Year to date:
  • Site-wide: 132,379
• Since beginning of last month:
  • Site-wide: 27,920

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

• Downloaded 851 times
• Download rankings, all-time:
  • Site-wide: 51,144
  • In bioinformatics: 5,148
• Year to date:
  • Site-wide: 117,362
• Since beginning of last month:
  • Site-wide: 120,597

Compression of quantification uncertainty for scRNA-seq counts

• Downloaded 829 times
• Download rankings, all-time:
  • Site-wide: 53,216
  • In bioinformatics: 5,363
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 122,997

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

• Downloaded 781 times
• Download rankings, all-time:
  • Site-wide: 58,111
  • In bioinformatics: 5,684
• Year to date:
  • Site-wide: 87,610
• Since beginning of last month:
  • Site-wide: 184,126

Assessing exposure effects on gene expression

• Downloaded 780 times
• Download rankings, all-time:
  • Site-wide: 58,192
  • In genomics: 4,099
• Year to date:
  • Site-wide: 116,594
• Since beginning of last month:
  • Site-wide: 103,386

Gene-level germline contributions to clinical risk of recurrence scores in Black and White breast cancer patients

• Downloaded 743 times
• Download rankings, all-time:
  • Site-wide: 62,580
  • In genetic and genomic medicine: 392
• Year to date:
  • Site-wide: 102,615
• Since beginning of last month:
  • Site-wide: 113,016

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

• Downloaded 692 times
• Download rankings, all-time:
  • Site-wide: 69,383
  • In bioinformatics: 6,521
• Year to date:
  • Site-wide: 116,254
• Since beginning of last month:
  • Site-wide: 200,667

Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

• Downloaded 621 times
• Download rankings, all-time:
  • Site-wide: 79,988
  • In bioinformatics: 7,365
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 84,061

Detecting isoform-level allelic imbalance accounting for inferential uncertainty

• Downloaded 618 times
• Download rankings, all-time:
  • Site-wide: 80,642
  • In bioinformatics: 7,563
• Year to date:
  • Site-wide: 40,556
• Since beginning of last month:
  • Site-wide: 22,698

DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing

• Downloaded 577 times
• Download rankings, all-time:
  • Site-wide: 87,945
  • In bioinformatics: 7,936
• Year to date:
  • Site-wide: 67,984
• Since beginning of last month:
  • Site-wide: 123,504

Silhouette width using generalized mean - a flexible method for assessing clustering efficiency

• Downloaded 558 times
• Download rankings, all-time:
  • Site-wide: 91,749
  • In bioinformatics: 8,168
• Year to date:
  • Site-wide: 73,526
• Since beginning of last month:
  • Site-wide: 140,932

Inferring cell-type-specific causal gene regulatory networks during human neurogenesis

• Downloaded 544 times
• Download rankings, all-time:
  • Site-wide: 94,624
  • In genomics: 5,911
• Year to date:
  • Site-wide: 81,058
• Since beginning of last month:
  • Site-wide: 86,966

Inference of cell-type specific imprinted regulatory elements and genes during human neuronal differentiation

• Downloaded 538 times
• Download rankings, all-time:
  • Site-wide: 95,897
  • In genomics: 5,951
• Year to date:
  • Site-wide: 59,322
• Since beginning of last month:
  • Site-wide: 63,086

ACTOR: a latent Dirichlet model to compare expressed isoform proportions to a reference panel

• Downloaded 533 times
• Download rankings, all-time:
  • Site-wide: 96,807
  • In bioinformatics: 8,496
• Year to date:
  • Site-wide: 144,091
• Since beginning of last month:
  • Site-wide: 128,007

Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu

• Downloaded 447 times
• Download rankings, all-time:
  • Site-wide: 117,289
  • In bioinformatics: 11,125
• Year to date:
  • Site-wide: 2,183
• Since beginning of last month:
  • Site-wide: 3,410

A framework for transcriptome-wide association studies in breast cancer in diverse study populations

• Downloaded 436 times
• Download rankings, all-time:
  • Site-wide: 119,985
  • In cancer biology: 3,626
• Year to date:
  • Site-wide: 166,542
• Since beginning of last month:
  • Site-wide: 187,208

bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing

• Downloaded 379 times
• Download rankings, all-time:
  • Site-wide: 136,257
  • In bioinformatics: 11,245
• Year to date:
  • Site-wide: 188,215
• Since beginning of last month:
  • Site-wide: 19,359

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

• Downloaded 376 times
• Download rankings, all-time:
  • Site-wide: 137,185
  • In bioinformatics: 12,050
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 7,849

Evaluating brain structure traits as endophenotypes using polygenicity and discoverability

• Downloaded 249 times
• Download rankings, all-time:
  • Site-wide: 174,942
  • In genetics: 6,329
• Year to date:
  • Site-wide: 122,744
• Since beginning of last month:
  • Site-wide: 162,180

Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features

• Downloaded 225 times
• Download rankings, all-time:
  • Site-wide: 181,414
  • In genomics: 9,012
• Year to date:
  • Site-wide: 8,224
• Since beginning of last month:
  • Site-wide: 18,813

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

• Downloaded 185 times
• Download rankings, all-time:
  • Site-wide: 191,111
  • In bioinformatics: 14,456
• Year to date:
  • Site-wide: 8,353
• Since beginning of last month:
  • Site-wide: 5,792

TreeTerminus - Creating transcript trees using inferential replicate counts

• Downloaded 137 times
• Download rankings, all-time:
  • Site-wide: 200,707
  • In bioinformatics: 14,738
• Year to date:
  • Site-wide: 177,444
• Since beginning of last month:
  • Site-wide: 41,477

Assessing Etiologic Heterogeneity for Multinomial Outcome with Two-Phase Outcome-Dependent Sampling Design

• Downloaded 83 times
• Download rankings, all-time:
  • Site-wide: 210,714
  • In epidemiology: 8,151
• Year to date:
  • Site-wide: 176,832
• Since beginning of last month:
  • Site-wide: 58,613