David R. Lougheed
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View article: STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation
STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation Open
Variation in short tandem repeats (STRs) is implicated in Mendelian disease and complex traits, but can be difficult to resolve with short-read genome sequencing. We present STRkit , a software package for genotyping STRs using long read s…
View article: Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs
Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs Open
Freshwater ecosystems are complex, diverse, and face multiple imminent threats that have led to changes in both structure and function. It is urgent that we develop and standardize monitoring tools that allow for rapid and comprehensive as…
View article: EpiVar Browser: advanced exploration of epigenomics data under controlled access
EpiVar Browser: advanced exploration of epigenomics data under controlled access Open
Motivation Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, s…
View article: How to barcode (almost all) freshwater biodiversity
How to barcode (almost all) freshwater biodiversity Open
Freshwater ecosystems are complex, diverse and face a variety of imminent threats that have led to changes in both ecosystem structure and function. It is urgent that we develop and standardize monitoring tools allowing for rapid and compr…
View article: EpiVar Browser: advanced exploration of epigenomics data under controlled access
EpiVar Browser: advanced exploration of epigenomics data under controlled access Open
Motivation Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, s…
View article: RNAget: an API to securely retrieve RNA quantifications
RNAget: an API to securely retrieve RNA quantifications Open
Summary Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in ma…
View article: Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection Open
Summary Humans display remarkable inter-individual variation in immune response when exposed to identical immune challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here …
View article: <i>baRcodeR</i> : An open‐source R package for sample labelling
<i>baRcodeR</i> : An open‐source R package for sample labelling Open
Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Open‐source tools aid the reproducibility of data analysis, but analogous …
View article: Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations
Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations Open
The functional effect of a gene edit by designer nucleases depends on the DNA repair outcome at the targeted locus. While non-homologous end joining (NHEJ) repair results in various mutations, microhomology-mediated end joining (MMEJ) crea…
View article: baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science
baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science Open
Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Several flexible, open-source tools developed for the R and Python coding …
View article: Un nouveau chapitre.
Un nouveau chapitre. Open