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miscrefs.bib
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miscrefs.bib
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@misc{socialstyrelsen-2018,
author = {{Socialstyrelsen}},
title = {Cancer i siffror 2018},
note = {\url{https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/statistik/2018-6-10.pdf}, visited 2020-11-15}
}
@misc{socialstyrelsen-db,
author = {{Socialstyrelsen}},
title = {Socialstyrelsen Cancer Statistics Database},
note = {\url{https://sdb.socialstyrelsen.se/if_can/}, visited 2020-11-16}
}
@misc{seer-db,
author = {{U.S. National Cancer Institute}},
title = {Surveillance, Epidemiology, and End Results (SEER) Program},
note = {\url{https://seer.cancer.gov/}, visited 2020-11-20}
}
@misc{bioinf-career,
author = {Chang, Jeffrey},
title = {Core services: Reward bioinformaticians},
note = {\url{https://www.nature.com/news/core-services-reward-bioinformaticians-1.17251}, visited 2020-11-24}
}
@mastersthesis{Brueffer:2013,
author = {Brueffer, Christian},
title = {{Quality Control and Analysis of RNA-seq Data from Breast
Cancer Tumor Samples}},
school = {Lund University, Department of Biology},
year = 2013,
month = 7,
}
@article{Dahlgren:2020,
author = {Dahlgren, Malin and George, Anthony M and Brueffer, Christian and Gladchuk, Sergii and Chen, Yilun and Vallon-Christersson, Johan and Hegardt, Cecilia and Häkkinen, Jari and Rydén, Lisa and Malmberg, Martin and Larsson, Christer and Gruvberger-Saal, Sofia and Ehinger, Anna and Loman, Niklas and Borg, Åke and Saal, Lao H},
title = {Pre-existing somatic mutations of estrogen receptor alpha (ESR1) in early-stage primary breast cancer},
Journal = {Manuscript}
}
@misc{who-icd-o,
author = {{World Health Organization}},
title = {International Classification of Diseases for Oncology (ICD-O) -- 3rd Ed., 1st Rev.},
note = {\url{https://apps.who.int/iris/handle/10665/96612}, visited 2020-11-30},
}
@misc{two-color-chemistry,
author = {Andrews, Simon},
title = {Illumina 2 colour chemistry can overcall high confidence G bases},
note = {\url{https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/}, visited 2020-11-25},
}
@misc{czi,
author = {{Chan Zuckerberg Initiative}},
title = {Essential Open Source Software for Science},
note = {\url{https://chanzuckerberg.com/eoss/}, visited 2020-11-15}
}
@misc{rse,
author = {{Research Software Engineers International}},
note = {\url{https://researchsoftware.org/}, visited 2020-11-15}
}
@misc{conda-forge,
author = {{conda-forge}},
title = {A community-led collection of recipes, build infrastructure and distributions for the conda package manager.},
note = {\url{https://conda-forge.org/}, visited 2020-11-15}
}
@misc{illumina-base-qual,
author = {{Illumina Inc.}},
title = {Technical Note: Quality Scores for Next-Generation Sequencing},
note = {\url{https://www.illumina.com/documents/products/technotes/technote_Q-Scores.pdf}, visited 2020-11-24},
}
@misc{illumina-ht12-sheet,
author = {{Illumina Inc.}},
title = {{Illumina HumanHT-12 v4 BeadChip Product Information Sheet}},
note = {\url{https://www.illumina.com/documents/products/product_information_sheets/product_info_humanht-12.pdf}, visited 2020-08-06},
}
@misc{illumina-market-share,
author = {{UK Competition \& Market Authority}},
title = {Looking forward to the future: investigating the proposed acquisition of PacBio by Illumina },
note = {\url{https://www.gov.uk/government/publications/analysis-of-the-investigation-of-the-proposed-acquisition-of-pacbio-by-illumina/looking-forward-to-the-future-investigating-the-proposed-acquisition-of-pacbio-by-illumina}, visited 2020-08-26},
}
@misc{gatk-best-practices,
author = {{GATK Best Practices}},
note = {\url{https://gatk.broadinstitute.org/hc/en-us/articles/360035894751}},
}
@article{genefu,
author = {{Gendoo, D. M. and Ratanasirigulchai, N. and Schroeder, M. S. and Pare, L. and Parker, Joel S. and Prat, A. and Haibe-Kains, B.}},
Title = {genefu: Computation of Gene Expression-Based Signatures in Breast Cancer},
note = {\url{http://www.pmgenomics.ca/bhklab/software/genefu}}
}
@misc{fastqc,
author = {{FastQC}},
note = {\url{https://www.bioinformatics.babraham.ac.uk/projects/fastqc/}},
}
@misc{picard,
author = {{Picard}},
note = {\url{https://broadinstitute.github.io/picard}},
}
@misc{umis,
author = {{umis}},
note = {\url{https://github.com/vals/umis}},
}
@misc{fgbio,
author = {{fgbio}},
note = {\url{https://github.com/fulcrumgenomics/fgbio}},
}
@misc{pysam,
author = {{pysam}},
note = {\url{https://github.com/pysam-developers/pysam}},
}
@misc{repeatmasker,
author = {{Smit, AFA and Hubley, R and Green, P}},
title = {{RepeatMasker Open-4.0}},
note = {\url{http://www.repeatmasker.org}},
}
@misc{bcbio-nextgen,
author = {{bcbio-nextgen}},
note = {\url{https://github.com/bcbio/bcbio-nextgen}},
}
@misc{pamr,
author = {{pamr}},
note = {\url{https://cran.r-project.org/web/packages/pamr/}},
}
@misc{sam-format,
author = {{The SAM/BAM Format Specification Working Group}},
title = {{Sequence Alignment/Map Format Specification}},
note = {\url{https://samtools.github.io/hts-specs/SAMv1.pdf}},
}