SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python.

Johannes Rainer

Marilyn De Graeve Wout Bittremieux Thomas Naake Carolin Huber Matthias Anagho-Mattanovich Nils Hoffmann Pierre Marchal Victor Chrone Philippine Louail Helge Hecht Michael Witting Johannes Rainer SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. 8070 2025 June 10 J. Open Source Softw. 110 https://doi.org/10.21105/joss.08070 db/journals/jossw/jossw10.html#GraeveBNHAHMCLHWR25 streams/journals/jossw

Charlotte Soneson Lori A. Shepherd Marcel Ramos Kevin C. Rue-Albrecht Johannes Rainer Hervé Pagès Vincent J. Carey Eleven quick tips for writing a Bioconductor package. 1012856 2025 21 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1012856 db/journals/ploscb/ploscb21.html#SonesonSRRRPC25 streams/journals/ploscb

Thomas Naake Johannes Rainer Wolfgang Huber MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. 2023 October 39 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btad618 db/journals/bioinformatics/bioinformatics39.html#NaakeRH23

Christian X. Weichenberger Johannes Rainer Cristian Pattaro Peter P. Pramstaller Francisco S. Domingues Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. 69-76 2019 35 Bioinform. 1 https://doi.org/10.1093/bioinformatics/bty541 https://www.wikidata.org/entity/Q90237901 db/journals/bioinformatics/bioinformatics35.html#WeichenbergerRP19

Johannes Rainer Laurent Gatto Christian X. Weichenberger ensembldb: an R package to create and use Ensembl-based annotation resources. 3151-3153 2019 35 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btz031 https://www.wikidata.org/entity/Q91250541 db/journals/bioinformatics/bioinformatics35.html#RainerGW19

Johannes Rainer Daniel Taliun Yuri D'Elia Cristian Pattaro Francisco S. Domingues Christian X. Weichenberger FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees. 1583-1585 2016 32 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btw019 https://www.wikidata.org/entity/Q40069583 db/journals/bioinformatics/bioinformatics32.html#RainerTDPDW16

Johannes Rainer Fátima Sánchez-Cabo Gernot Stocker Alexander Sturn Zlatko Trajanoski CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. 498-503 2006 34 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkl038 https://www.wikidata.org/entity/Q31048899 db/journals/nar/nar34.html#RainerSSST06

Alexander Sturn Bernhard Mlecnik Roland Pieler Johannes Rainer Thomas Truskaller Zlatko Trajanoski Client-Server environment for high-performance gene expression data analysis. 772-773 2003 19 Bioinform. 6 db/journals/bioinformatics/bioinformatics19.html#SturnMPRTT03 https://doi.org/10.1093/bioinformatics/btg074 https://www.wikidata.org/entity/Q30725017

Johannes Rainer Software validation with CASE-TOOLS. 240-249 1993 SAFECOMP https://doi.org/10.1007/978-1-4471-2061-2_25 conf/safecomp/1993 db/conf/safecomp/safecomp1993.html#Rainer93 Matthias Anagho-Mattanovich Wout Bittremieux Vincent CareyVincent J. Carey Victor Chrone Yuri D'Elia Francisco S. Domingues Laurent Gatto Marilyn De Graeve Helge Hecht Nils Hoffmann Carolin Huber Wolfgang Huber Philippine Louail Pierre Marchal Bernhard Mlecnik Thomas Naake Hervé Pagès Cristian Pattaro Roland Pieler Peter P. Pramstaller Marcel Ramos Kevin C. Rue-Albrecht Fátima Sánchez-Cabo Lori A. Shepherd Charlotte Soneson Gernot Stocker Alexander Sturn Daniel Taliun Zlatko Trajanoski Thomas Truskaller Christian X. Weichenberger Michael Witting