cran: BiocManager | Projects | Ecosyste.ms: Papers

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.3390/microorganisms7110547

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests
Cited by: 9
Author(s): Christina Weißbecker, Anna Heintz‐Buschart, Helge Bruelheide, François Buscot, Tesfaye Wubet
Software Mentions: 19
Published: about 5 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 3 years ago

10.3389/fonc.2021.560136

Screening of miRNAs as Prognostic Biomarkers for Colon Adenocarcinoma and Biological Function Analysis of Their Target Genes
Cited by: 2
Author(s): Guoliang Zheng, Guojun Zhang, Yan Zhao, Zhichao Zheng
Software Mentions: 14
Published: over 3 years ago

10.3389/fmicb.2021.689262

Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018)
Cited by: 9
Author(s): Vicente Lopez-Chavarrias, María Ugarte‐Ruiz, Carmen Bárcena, Adolfo Olarra, María Teresa Antonio García, José Luís Saez, Cristina de Frutos, Tania Serrano, I. Abad Perez, M. Moreno, Lucas Domı́nguez, Julio Álvarez
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.24187.2

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
Cited by: 0
Author(s): Charlotte Soneson, Fédérico Marini, Florian Geier, Michael I. Love, Michael Stadler
Software Mentions: 12
Published: about 4 years ago

10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago

10.12688/f1000research.26771.2

HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
Cited by: 1
Author(s): Tim O. Nieuwenhuis, Marc K. Halushka
Software Mentions: 11
Published: over 3 years ago

10.3389/pore.2021.594649

Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis
Cited by: 7
Author(s): Xi Zhang, Junjun Zhang, Yang Liu, Jie Li, Juan Tan, Zewen Song
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2020.00260

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix
Cited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 4 years ago

10.12688/f1000research.17976.2

TFutils: Data structures for transcription factor bioinformatics
Cited by: 2
Author(s): Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin A. Raby, Vincent J. Carey
Software Mentions: 10
Published: over 5 years ago

10.1155/2021/7408893

Identification of a Four-lncRNA Prognostic Signature for Colon Cancer Based on Genome Instability
Cited by: 2
Author(s): Duo Yun, Zhimin Yang
Software Mentions: 9
Published: about 3 years ago

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: almost 4 years ago

10.26508/lsa.202000757

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
Cited by: 16
Author(s): Aditya Bhagwat, Johannes Graumann, René Wiegandt, Mette Bentsen, Jordan M. Welker, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso
Software Mentions: 9
Published: about 4 years ago

10.7717/peerj.11233

Identification of a ferroptosis-related gene signature (FRGS) for predicting clinical outcome in lung adenocarcinoma
Cited by: 11
Author(s): Sheng Wang, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 8
Published: over 3 years ago

10.3390/vaccines9030217

HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment
Cited by: 2
Author(s): Maria Röhl, Annelie Tjernlund, Julie Lajoie, Gabriella Edfeldt, Frideborg Bradley, Sofia Bergström, Vilde Kaldhusdal, Alexandra Åhlberg, Anna Månberg, Kenneth Omollo, Geneviève Boily-Larouche, Muhammad Asghar, Douglas S. Kwon, Julius Oyugi, Joshua Kimani, Peter Nilsson, Keith R. Fowke, Kristina Broliden
Software Mentions: 8
Published: over 3 years ago

10.3389/fonc.2020.01411

Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With Prognosis
Cited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: over 4 years ago

10.1155/2021/5538643

A Network Pharmacology and Molecular Docking Strategy to Explore Potential Targets and Mechanisms Underlying the Effect of Curcumin on Osteonecrosis of the Femoral Head in Systemic Lupus Erythematosus
Cited by: 4
Author(s): Pan Kang, Zhigen Wu, Yue Zhong, Zihao Wang, Chi Zhou, Shaochuan Huo, Hai Bin Guo, Songtao Li, Kun Xu, Ling-yun Liu, Shuai Chen, Hong-Yu Tang, Haibin Wang
Software Mentions: 7
Published: about 3 years ago

10.12688/f1000research.19410.1

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem
Cited by: 0
Author(s): Shian Su, Vincent J. Carey, Lori Shepherd, Matthew E. Ritchie, Martin Morgan, Sean Davis
Software Mentions: 7
Published: over 5 years ago

10.3389/fphar.2020.00076

Efficacy of Chinese Herbal Formula Sini Zuojin Decoction in Treating Gastroesophageal Reflux Disease: Clinical Evidence and Potential Mechanisms
Cited by: 10
Author(s): Shaowei Li, Mengfen Huang, Guojing Wu, Wei-Han Huang, Zhanhui Huang, Xiaoqian Yang, Jinming Ou, Qipeng Wei, Chengli Liu, YU Shaoyuan
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0234669

netboxr: Automated discovery of biological process modules by network analysis in R
Cited by: 2
Author(s): Eric Minwei Liu, Augustin Luna, Guanlan Dong, Chris Sander
Software Mentions: 7
Published: about 4 years ago

10.1093/gigascience/giz107

A field guide for the compositional analysis of any-omics data
Cited by: 162
Author(s): Thomas P. Quinn, Ionas Erb, Gregory B. Gloor, Cédric Notredame, Mark F. Richardson, Tamsyn M. Crowley
Software Mentions: 6
Published: about 5 years ago

10.3390/ijms21061938

Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
Cited by: 8
Author(s): Dimitrios S. Kanakoglou, Theodora-Dafni Michalettou, Christina Vasileiou, Evangelos Gioukakis, Δωροθέα Μανέτα, Konstantinos Kyriakidis, Alexandros G. Georgakilas, Ioannis Michalopoulos
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-020-07118-4

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance
Cited by: 6
Author(s): Biruk A. Feyissa, Justin B. Renaud, Vida Nasrollahi, Susanne E. Kohalmi, Abdelali Hannoufa
Software Mentions: 4
Published: about 4 years ago

10.1186/s13550-020-00632-2

A pan-cancer analysis of the clinical and genetic portraits of somatostatin receptor expressing tumor as a potential target of peptide receptor imaging and therapy
Cited by: 11
Author(s): Hyun-Jong Lee, Minseok Suh, Hongyoon Choi, Seunggyun Ha, Jin Chul Paeng, Gi Jeong Cheon, Keon Wook Kang, Dong Hoon Lee
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.8383

Autophagy-related genes prognosis signature as potential predictive markers for immunotherapy in hepatocellular carcinoma
Cited by: 23
Author(s): Deli Mao, Zhe Zhang, Xin Zhao, Xiaoqiang Dong
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.103491

Genome-wide analyses of the prognosis-related mRNA alternative splicing landscape and novel splicing factors based on large-scale low grade glioma cohort
Cited by: 8
Author(s): Wangrui Liu, Chuanyu Li, Wenhao Xu, Xiaojuan Liu, Hai-Dan Tang, Haiyang Huang
Software Mentions: 3
Published: over 4 years ago

10.1111/jcmm.15015

Prognostic value of the expression of chemokines and their receptors in regional lymph nodes of melanoma patients
Cited by: 10
Author(s): Ting‐feng Xiong, Fuqiang Pan, Qian Liang, Ruijin Luo, Dong Liu, Haiyan Mo, Xiang Zhou
Software Mentions: 2
Published: almost 5 years ago

10.1155/2021/9941791

Network Pharmacology and Molecular Docking Study on the Potential Mechanism of Yi-Qi-Huo-Xue-Tong-Luo Formula in Treating Diabetic Peripheral Neuropathy
Cited by: 13
Author(s): Yixuan Lin, Chuqiao Shen, Fanjing Wang, Zhaohui Fang, Guo-Ming Shen
Software Mentions: 2
Published: over 3 years ago

10.1186/s13568-020-01147-8

Effects of corn steep liquor on β-poly(l-malic acid) production in Aureobasidium melanogenum
Cited by: 5
Author(s): Genan Wang, Bingyi Shi, Pan Zhang, Tingbin Zhao, Hui Yin, Changsheng Qiao
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-82450-7

Involvement of the miR156/SPL module in flooding response in Medicago sativa
Cited by: 19
Author(s): Biruk A. Feyissa, Lisa Amyot, Vida Nasrollahi, Y. A. Papadopoulos, Susanne E. Kohalmi, Abdelali Hannoufa
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-83120-4

Development of an immune-related gene pairs signature for predicting clinical outcome in lung adenocarcinoma
Cited by: 6
Author(s): Chunlei Wu, Quanteng Hu, Dehua Mao
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: cran: BiocManager

Papers Mentioning BiocManager 35