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Biotite: new tools for a versatile Python bioinformatics library
Kunzmann, Patrick, Müller, Tom David, Greil, Maximilian, Krumbach, Jan Hendrik, Anter, Jacob Marcel, Bauer, Daniel, Islam, Faisal, Hamacher, Kay
Published in BMC bioinformatics (05.06.2023)
Published in BMC bioinformatics (05.06.2023)
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Journal Article
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS
Johnson, Jeanette A. I., Tsang, Ashley P., Mitchell, Jacob T., Zhou, David L., Bowden, Julia, Davis-Marcisak, Emily, Sherman, Thomas, Liefeld, Ted, Loth, Melanie, Goff, Loyal A., Zimmerman, Jacquelyn W., Kinny-Köster, Ben, Jaffee, Elizabeth M., Tamayo, Pablo, Mesirov, Jill P., Reich, Michael, Fertig, Elana J., Stein-O’Brien, Genevieve L.
Published in Nature protocols (01.12.2023)
Published in Nature protocols (01.12.2023)
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Journal Article
RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis
Sen, Samyabrata, Vairagare, Indraneel, Gosai, Jitendrapuri, Shrivastava, Abhishek
Published in BMC bioinformatics (18.05.2025)
Published in BMC bioinformatics (18.05.2025)
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Journal Article
PyNoetic: A modular python framework for no-code development of EEG brain-computer interfaces
Singh, Gursimran, Chharia, Aviral, Upadhyay, Rahul, Kumar, Vinay, Longo, Luca
Published in PloS one (06.08.2025)
Published in PloS one (06.08.2025)
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Journal Article
OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
Piquer-Esteban, Samuel, Arnau, Vicente, Diaz, Wladimiro, Moya, Andrés
Published in BMC bioinformatics (09.05.2024)
Published in BMC bioinformatics (09.05.2024)
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Journal Article
PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data
Georgi, Benjamin, Costa, Ivan Gesteira, Schliep, Alexander
Published in BMC bioinformatics (06.01.2010)
Published in BMC bioinformatics (06.01.2010)
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Journal Article
Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison
Kuijpers, Lucas, Hornung, Bastian, van den Hout - van Vroonhoven, Mirjam C. G. N., van IJcken, Wilfred F. J., Grosveld, Frank, Mulugeta, Eskeatnaf
Published in BMC genomics (12.04.2024)
Published in BMC genomics (12.04.2024)
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Journal Article
Image processing for electron microscopy single-particle analysis using XMIPP
Scheres, Sjors H W, Núñez-Ramírez, Rafael, Sorzano, Carlos O S, Carazo, José María, Marabini, Roberto
Published in Nature protocols (01.06.2008)
Published in Nature protocols (01.06.2008)
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Journal Article
GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array
Suzuki, Shuji, Kakuta, Masanori, Ishida, Takashi, Akiyama, Yutaka
Published in PloS one (06.08.2014)
Published in PloS one (06.08.2014)
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Journal Article
Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data
Li, Teng, Zou, Yiran, Li, Xianghan, Wong, Thomas K. F., Rodrigo, Allen G.
Published in BMC bioinformatics (27.09.2024)
Published in BMC bioinformatics (27.09.2024)
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Journal Article
Bioinformatic pipelines in Python with Leaf
Napolitano, Francesco, Mariani-Costantini, Renato, Tagliaferri, Roberto
Published in BMC bioinformatics (21.06.2013)
Published in BMC bioinformatics (21.06.2013)
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Journal Article