Open Source Software

The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and …
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
DOI PDF bioRxiv Preprint Code Dataset Press Release
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome
A crowdsourced set of curated structural variants for the human genome
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a …
Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook
DOI PDF bioRxiv Preprint Code
A crowdsourced set of curated structural variants for the human genome
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)
Background
Breast cancer is a disease of genomic alterations, of which the complete panorama of somatic mutations and how these relate …
Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
DOI
Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492)
Bioconda: sustainable and comprehensive software distribution for the life sciences
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multiplatform and …
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Devon Ryan, Anthony Bretaudeau, Gildas Le Corguillé, Christian Brueffer, et al
DOI bioRxiv Preprint Project Code
Bioconda: sustainable and comprehensive software distribution for the life sciences
TopHat-Recondition: A post-processor for TopHat unmapped reads
Background
TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version …
Christian Brueffer, Lao H. Saal
DOI PDF bioRxiv Preprint Code
TopHat-Recondition: A post-processor for TopHat unmapped reads
FreeBSD Security Event Auditing
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FreeBSD Security Event Auditing