Rxivist logo

Author: Michael Isaiah Love

Rankings

  • All-time downloads: 109,275 (rank: 1,889 )
  • Categories:
    • bioinformatics: 84,992 (rank: 14 )
    • cancer biology: 434 (rank: 36,412 (tie) )
    • epidemiology: 81 (rank: 43,649 (tie) )
    • genetic and genomic medicine: 736 (rank: 9,720 (tie) )
    • genetics: 4,641 (rank: 5,286 )
    • genomics: 17,489 (rank: 1,199 )

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 25,191 times
  • Download rankings, all-time:
    • 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

bioinformatics more details view paper
  • Downloaded 23,865 times
  • Download rankings, all-time:
    • 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

genomics more details view paper
  • Downloaded 7,342 times
  • Download rankings, all-time:
    • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genomics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genetics more details view paper
  • Downloaded 1,937 times
  • Download rankings, all-time:
    • 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

bioinformatics more details view paper
  • Downloaded 1,909 times
  • Download rankings, all-time:
    • 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

genomics more details view paper
  • 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

genomics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genomics more details view paper
  • 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

genetics more details view paper
  • 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

genetics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genomics more details view paper
  • 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

genetic and genomic medicine more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genomics more details view paper
  • 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

genomics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

cancer biology more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

genetics more details view paper
  • 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

genomics more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

epidemiology more details view paper
  • 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

PanLingua

News