Eleven quick tips for writing a Bioconductor package. by Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J Carey

Get full text

Learning and teaching biological data science in the Bioconductor community. by Jenny Drnevich, Frederick J Tan, Fabricio Almeida-Silva, Robert Castelo, Aedin C Culhane, Sean Davis, Maria A Doyle, Ludwig Geistlinger, Andrew R Ghazi, Susan Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin Rue-Albrecht, David J H Shih, Laurent Gatto, Charlotte Soneson

“…In this article, we provide an overview of key resources and best practices available within the Bioconductor project-an open-source software community focused on omics data analysis. …”
Get full text

scQTLtools: An R/Bioconductor Package for Comprehensive Identification and Visualization of Single-Cell eQTLs by Xiaofeng Wu, Xin Huang, Pinjing Chen, Jingtong Kang, Jin Yang, Zhanpeng Huang, Siwen Xu

Subjects: Get full text

tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography. by Ryosuke Matsuzawa, Daichi Kawahara, Makoto Kashima, Hiromi Hirata, Haruka Ozaki

“…R package tomoseqr is available on Bioconductor (https://doi.org/doi:10.18129/B9.bioc.tomoseqr) and GitHub (https://github.com/bioinfo-tsukuba/tomoseqr).…”
Get full text

Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective by Chu Pan, Yanlin Chen

“…Informeasure is available as an R/Bioconductor package at https://bioconductor.org/packages/Informeasure .…”
Get full text

Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells by Rodrigo Arcoverde Cerveira, Klara Lenart, Marcel Martin, Matthew James Hinchcliff, Fredrika Hellgren, Kewei Ye, Juliana Assis Geraldo, Taras Kreslavsky, Sebastian Ols, Karin Loré

Subjects: Get full text

A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor [version 2; peer review: 2 approved] by Kelsey Breslin, Shian Su, Tamara Cameron, James Lancaster, Lucinda Xiao, Matthew E. Ritchie, Peter F. Hickey, Quentin Gouil, Marnie E. Blewitt

Subjects: Get full text

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines [version 1; peer review: 2 approved] by Sean Davis, Marcel Ramos, Michael C. Schatz, Kai Gravel-Pucillo, Levi Waldron, Sehyun Oh, Martin Morgan, Vincent Carey

Subjects: Get full text

CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments by Ashley J. Waardenberg, Bassett Maya, Romaric Bouveret, Richard P. Harvey

“…CompGO is freely available as a R/Bioconductor package enabling easy integration into existing pipelines and is available at: http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.html…”
Get full text

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. by Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa, Raphael Gottardo

“…The substantial improvements to the core BioConductor flow cytometry packages give OpenCyto the potential for wide adoption. …”
Get full text

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. by Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphael Gottardo

“…Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data.…”
Get full text

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. by Borbala Mifsud, Inigo Martincorena, Elodie Darbo, Robert Sugar, Stefan Schoenfelder, Peter Fraser, Nicholas M Luscombe

“…GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).…”
Get full text

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm. by Robert Darkins, Emma J Cooke, Zoubin Ghahramani, Paul D W Kirk, David L Wild, Richard S Savage

“…The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. …”
Get full text

Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age by Xiaolong Guo, Mahnoor Sulaiman, Alexander Neumann, Shijie C. Zheng, Charlotte A.M. Cecil, Andrew E. Teschendorff, Bastiaan T. Heijmans

“…The UniLIFE panel and algorithms to estimate cell-type fractions are available from our EpiDISH Bioconductor R-package: https://bioconductor.org/packages/release/bioc/html/EpiDISH.html…”
Get full text

A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles. by Robert Stojnic, Audrey Qiuyan Fu, Boris Adryan

“…Both methods are implemented in the R package ddgraph, available as part of Bioconductor (http://bioconductor.org/packages/2.11/bioc/html/ddgraph.html). …”
Get full text

An R package for divergence analysis of omics data. by Wikum Dinalankara, Qian Ke, Donald Geman, Luigi Marchionni

“…The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. …”
Get full text

Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization by Michelle Pistner Nixon, Gregory B. Gloor, Justin D. Silverman

“…We introduce updates to the popular ALDEx2 software package, available on Bioconductor, facilitating scale model analysis.…”
Get full text

Lung Cancer Biomarker Identification from Differential Expression Analysis Using RNA-Seq Data for Designing Multitargeted Drugs by Syed Naseer Ahmad Shah, Rafat Parveen

“…We analysed RNA sequencing on lung cancer samples from NCBI’s SRA database. Using Bioconductor in R, we identified key genes, including hub genes TOP2A and TMEM100, crucial for cellular processes. …”
Get full text

Gene expression study in retinoblastoma patients with different anaplasias and lateralities by Wan Li, Kangkang Xu, Fei Chen

“…After grouping by anaplasia or laterality, the data were reanalyzed with Student’s t-test in R and Bioconductor software. The functional enrichment of genes significantly related to anaplasia and laterality was explored via GSEA. …”
Get full text

Efficient and easy gene expression and genetic variation data analysis and visualization using exvar by Hiba Ben Aribi, Imraan Dixon, Najla Abassi, Olaitan I. Awe

“…We developed a novel R package using multiple Cran and Bioconductor packages to perform gene expression analysis and genetic variant calling from RNA sequencing data. …”
Get full text