相似文献
1
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Bioinformatics. 2010 Nov 1;26(21):2792-3. doi: 10.1093/bioinformatics/btq503. Epub 2010 Sep 1.
2
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.
Bioinformatics. 2012 Nov 1;28(21):2858-9. doi: 10.1093/bioinformatics/bts530. Epub 2012 Sep 3.
3
Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.
Methods Mol Biol. 2014;1101:87-112. doi: 10.1007/978-1-62703-721-1_6.
4
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058.
5
Importing ArrayExpress datasets into R/Bioconductor.
Bioinformatics. 2009 Aug 15;25(16):2092-4. doi: 10.1093/bioinformatics/btp354. Epub 2009 Jun 8.
6
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures.
BMC Bioinformatics. 2020 Oct 14;21(1):453. doi: 10.1186/s12859-020-03796-9.
7
Working with Oligonucleotide Arrays.
Methods Mol Biol. 2016;1418:145-59. doi: 10.1007/978-1-4939-3578-9_7.
8
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.
Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23.
9
Libaffy: software for processing Affymetrix GeneChip data.
Bioinformatics. 2007 Jun 15;23(12):1562-4. doi: 10.1093/bioinformatics/btm127. Epub 2007 Apr 26.
10
WGCNA: an R package for weighted correlation network analysis.
BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.
引用本文的文献
1
Neoadjuvant immunotherapy promotes the formation of mature tertiary lymphoid structures in a remodeled pancreatic tumor microenvironment.
Cancer Immunol Res. 2025 Aug 15. doi: 10.1158/2326-6066.CIR-25-0387.
2
Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.
Genome Med. 2025 Aug 7;17(1):87. doi: 10.1186/s13073-025-01502-z.
3
MOTL: enhancing multi-omics matrix factorization with transfer learning.
Genome Biol. 2025 Jul 25;26(1):224. doi: 10.1186/s13059-025-03675-7.
4
Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia.
JCI Insight. 2025 Jun 26;10(15). doi: 10.1172/jci.insight.191595. eCollection 2025 Aug 8.
5
mNSF: multi-sample non-negative spatial factorization.
Genome Biol. 2025 Jun 2;26(1):149. doi: 10.1186/s13059-025-03601-x.
6
Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades.
Sci Rep. 2024 Oct 17;14(1):24360. doi: 10.1038/s41598-024-74324-5.
7
PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration.
Cell Syst. 2024 Aug 21;15(8):753-769.e5. doi: 10.1016/j.cels.2024.07.001. Epub 2024 Aug 7.
8
Multi-sample non-negative spatial factorization.
bioRxiv. 2024 Nov 27:2024.07.01.599554. doi: 10.1101/2024.07.01.599554.
9
Interface-guided phenotyping of coding variants in the transcription factor RUNX1.
Cell Rep. 2024 Jul 23;43(7):114436. doi: 10.1016/j.celrep.2024.114436. Epub 2024 Jul 4.
10
Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation.
Sci Immunol. 2024 Jun 28;9(96):eadk4893. doi: 10.1126/sciimmunol.adk4893.
本文引用的文献
1
High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics.
J Am Stat Assoc. 2008 Dec 1;103(484):1438-1456. doi: 10.1198/016214508000000869.
2
Asymptotic conditional singular value decomposition for high-dimensional genomic data.
Biometrics. 2011 Jun;67(2):344-52. doi: 10.1111/j.1541-0420.2010.01455.x. Epub 2010 Jun 16.
3
Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data.
Cancer Res. 2009 Dec 1;69(23):9125-32. doi: 10.1158/0008-5472.CAN-09-1709. Epub 2009 Nov 10.
4
Matrix factorization for recovery of biological processes from microarray data.
Methods Enzymol. 2009;467:59-77. doi: 10.1016/S0076-6879(09)67003-8.
5
Analyzing gene expression data in terms of gene sets: methodological issues.
Bioinformatics. 2007 Apr 15;23(8):980-7. doi: 10.1093/bioinformatics/btm051. Epub 2007 Feb 15.
6
Determination of strongly overlapping signaling activity from microarray data.
BMC Bioinformatics. 2006 Feb 28;7:99. doi: 10.1186/1471-2105-7-99.
7
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate.
Nucleic Acids Res. 2003 Jul 1;31(13):3775-81. doi: 10.1093/nar/gkg624.
8
Learning the parts of objects by non-negative matrix factorization.
Nature. 1999 Oct 21;401(6755):788-91. doi: 10.1038/44565.
9
Systematic determination of genetic network architecture.
Nat Genet. 1999 Jul;22(3):281-5. doi: 10.1038/10343.
10
A new method for spectral decomposition using a bilinear Bayesian approach.
J Magn Reson. 1999 Mar;137(1):161-76. doi: 10.1006/jmre.1998.1639.
Zotero 插件