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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344

Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468

Huber W, et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115-121; doi:10.1038/nmeth.3252 (full-text free with registration).

Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi: 10.1371/journal.pcbi.1003118

Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2019-09-17T17:40:07-04:00.

Bais AS, Kostka D. scds: Computational Annotation of Doublets in Single-Cell RNA Sequencing Data. Bioinformatics. doi:10.1093/bioinformatics/btz698 (10 September 2019)

Tran AN, Dussaq AM, Kennell T Jr, Willey CD, Hjelmeland AB. HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data. BMC Bioinformatics, 20(1), pp. 463. doi:10.1186/s12859-019-3059-z (9 September 2019)

Li Z, Wu H. TOAST: improving reference-free cell composition estimation by cross-cell type differential analysis. Genome Biol, 20(1), pp. 190. doi:10.1186/s13059-019-1778-0 (4 September 2019)

Ceddia G, Martino LN, Parodi A, Secchi P, Campaner S, Masseroli M. Association rule mining to identify transcription factor interactions in genomic regions. Bioinformatics. doi:10.1093/bioinformatics/btz687 (3 September 2019)

Zhou XR, Song N, Luo JY, Zhai H, Li XM, Zhao Q, Liu F, Li XM, Yang YN. Expression profiles and potential functions of long non-coding RNA in stable angina pectoris patients from Uyghur population of China. Biosci Rep, 39(9). doi:10.1042/BSR20190364 (3 September 2019)

Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D. SigsPack, a package for cancer mutational signatures. BMC Bioinformatics, 20(1), pp. 450. doi:10.1186/s12859-019-3043-7 (2 September 2019)

Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics. doi:10.1093/bioinformatics/btz681 (30 August 2019)

Xu T, Jin P, Qin Z. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. Bioinformatics. doi:10.1093/bioinformatics/btz669 (27 August 2019)

Sánchez-Pla A, Salicrú M, Ocaña J. An equivalence approach to the integrative analysis of feature lists. BMC Bioinformatics, 20(1), pp. 441. doi:10.1186/s12859-019-3008-x (27 August 2019)

Tan G, Polychronopoulos D, Lenhard B. CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Comput Biol, 15(8), pp. e1006940. doi:10.1371/journal.pcbi.1006940 (26 August 2019)

Bernabeu A, Lledo B, Díaz MC, Lozano FM, Ruiz V, Fuentes A, Lopez-Pineda A, Moliner B, Castillo JC, Ortiz JA, Ten J, Llacer J, Carratala-Munuera C, Orozco-Beltran D, Quesada JA, Bernabeu R. Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment. J Assist Reprod Genet. doi:10.1007/s10815-019-01564-0 (24 August 2019)

da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L. CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics. doi:10.1093/bioinformatics/btz632 (8 August 2019)

Zhou D, Sun Y, Jia Y, Liu D, Wang J, Chen X, Zhang Y, Ma X. Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma. Oncol Lett, 18(4), pp. 3613-3622. doi:10.3892/ol.2019.10733 (7 August 2019)

Brionne A, Juanchich A, Hennequet-Antier C. ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity. BioData Min, 12, pp. 16. doi:10.1186/s13040-019-0204-1 (6 August 2019)

Van Aken B. Response to the note to editor: Comments on "transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)". Int J Phytoremediation, pp. 1-2. doi:10.1080/15226514.2019.1645090 (6 August 2019)

Sun J, Xu H, Qi M, Zhang C, Shi J. Identification of key genes in osteosarcoma by meta‑analysis of gene expression microarray. Mol Med Rep. doi:10.3892/mmr.2019.10543 (31 July 2019)

Huo Z, Tang S, Park Y, Tseng G. P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications. Bioinformatics. doi:10.1093/bioinformatics/btz589 (29 July 2019)

Reynès C, Kister G, Rohmer M, Bouschet T, Varrault A, Dubois E, Rialle S, Journot L, Sabatier R. ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses. Bioinformatics. doi:10.1093/bioinformatics/btz564 (26 July 2019)

Zimmermann MT, Kabat B, Grill DE, Kennedy RB, Poland GA. RITAN: rapid integration of term annotation and network resources. PeerJ, 7, pp. e6994. doi:10.7717/peerj.6994 (19 July 2019)

List M, Dehghani Amirabad A, Kostka D, Schulz MH. Large-scale inference of competing endogenous RNA networks with sparse partial correlation. Bioinformatics, 35(14), pp. i596-i604. doi:10.1093/bioinformatics/btz314 (15 July 2019)