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Author: Alicia Oshlack

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  • All-time downloads: 32,187 (rank: 1,435 out of 397,832)
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    • bioinformatics: 29,658 (rank: 81 out of 33,896)
    • developmental biology: 2,529 (rank: 598 (tie) out of 15,471)

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Preprints

A cross-package Bioconductor workflow for analysing methylation array data

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SuperTranscript: a data driven reference for analysis and visualisation of transcriptomes

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High throughput single cell RNA-seq of developing mouse kidney and human kidney organoids reveals a roadmap for recreating the kidney

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Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

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STRetch: detecting and discovering pathogenic short tandem repeats expansions

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Splatter: Simulation Of Single-Cell RNA Sequencing Data

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Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

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Ximmer: A System for Improving Accuracy and Consistency of CNV Calling from Exome Data

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SuperFreq: Integrated mutation detection and clonal tracking in cancer

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JAFFA: High sensitivity transcriptome-focused fusion gene detection.

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Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

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Bazam: A rapid method for read extraction and realignment of high throughput sequencing data

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Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

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Fast and accurate differential transcript usage by testing equivalence class counts

bioinformatics more details view paper
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Clinker: visualising fusion genes detected in RNA-seq data

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A comparison of control samples for ChIP-seq of histone modifications

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Cpipe: a shared variant detection pipeline designed for diagnostic settings

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MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

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Transcriptional evaluation of the developmental accuracy, reproducibility and robustness of kidney organoids derived from human pluripotent stem cells

bioinformatics more details view paper
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Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

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Gene Length And Detection Bias In Single Cell RNA Sequencing Protocols

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Pooled-parent exome sequencing to prioritise de novo variants in genetic disease

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DiffVar: A new method for detecting differential variability with application to methylation in cancer and aging

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Accuracy of short tandem repeats genotyping tools in whole exome sequencing data

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Detecting copy number alterations in RNA-Seq using SuperFreq

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