bioconductor: systemPipeR | Projects

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: about 3 years ago

10.3390/ijms22094531

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes
Cited by: 4
Author(s): Alexander V. Gopanenko, Alena V. Kolobova, Alexey E. Tupikin, Мarsel R. Kabilov, Alexey A. Malygin, Г. Г. Карпова
Software Mentions: 6
Published: over 3 years ago

10.1186/s13071-021-04717-2

Transcriptomic profiling of three-dimensional cholangiocyte spheroids long term exposed to repetitive Clonorchis sinensis excretory-secretory products
Cited by: 4
Author(s): Jung Woong Kim, Junyeong Yi, Jin‐Hong Park, Ji Hoon Jeong, Jin-Ho Kim, Jihee Won, Seok Chung, Tong Soo Kim, Jhang Ho Pak
Software Mentions: 6
Published: over 3 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 6 years ago

10.3390/genes12020264

Bisphenol A Exposure Changes the Transcriptomic and Proteomic Dynamics of Human Retinoblastoma Y79 Cells
Cited by: 7
Author(s): Chulhong Kim, Mi Jin Kim, Jin‐Hong Park, Jin-Ho Kim, Jiyoung Kim, Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: over 3 years ago

10.3390/genes12020201

Ablation of SMUG1 Reduces Cell Viability and Increases UVC-Mediated Apoptosis in Hepatocarcinoma HepG2 Cells
Cited by: 1
Author(s): Mi-Jin An, Geun-Seup Shin, Hyun-Min Lee, Jung-Woong Kim
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-016-0902-3

NEAT: a framework for building fully automated NGS pipelines and analyses
Cited by: 7
Author(s): Patrick Schorderet
Software Mentions: 5
Published: over 8 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-019-2676-x

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Cited by: 5
Author(s): Taewoon Joo, Ji-Hye Choi, Jihye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung, Hyun Goo Woo
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-017-1087-8

Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria
Cited by: 21
Author(s): Melania Abrahamian, Meenakshi S. Kagda, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.7501

Improvement of subsoil physicochemical and microbial properties by short-term fallow practices
Cited by: 4
Author(s): Guangyu Li, Walter Timo de Vries, Cifang Wu, Hongyu Zheng
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 8 years ago

10.3390/cells9051228

Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level
Cited by: 8
Author(s): Alexander V. Gopanenko, Alena V. Kolobova, Mariya I. Meschaninova, Alya G. Venyaminova, Alexey E. Tupikin, Мarsel R. Kabilov, Alexey A. Malygin, Г. Г. Карпова
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-6443-1

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid
Cited by: 32
Author(s): María Luisa Irigoyen, Danielle C. Garceau, Adriana Bohórquez-Chaux, Luís Augusto Becerra López-Lavalle, Laura Pérez-Fons, Paul D. Fraser, Linda L. Walling
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-59976-3

Immune correlates of postexposure vaccine protection against Marburg virus
Cited by: 18
Author(s): Courtney Woolsey, Allen Jankeel, Demetrius Matassov, Joan B. Geisbert, Krystle N. Agans, Viktoriya Borisevich, Robert W. Cross, Daniel J. Deer, Karla A. Fenton, Theresa Latham, Cheryl Gerardi, Chad E. Mire, John H. Eldridge, Ilhem Messaoudi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-92092-4

Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
Cited by: 0
Author(s): Ina Jungersen Andresen, Russell J. S. Orr, Anders K. Krabberød, Kamran Shalchian-Tabrizi, Jon Bråte
Software Mentions: 3
Published: over 3 years ago

10.1101/2021.01.19.426885

Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine
Cited by: 14
Author(s): Wakako Furuyama, Kyle Shifflett, Amanda N Pinksi, Amanda Griffin, Friederike Feldmann, Atsushi Okumura, Tylisha Gourdine, Allen Jankeel, Jamie Lovaglio, Patrick W. Hanley, Tina Thomas, Chad S. Clancy, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: over 3 years ago

10.1101/2021.07.11.451964

Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model
Cited by: 3
Author(s): Kyle L. O’Donnell, Amanda N. Pinski, Chad S. Clancy, Tylisha Gourdine, Kyle Shifflett, Paige Fletcher, Ilhem Messaoudi, Andrea Marzi
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2017.00335

CD103+ CD8 T Cells in the Toxoplasma-Infected Brain Exhibit a Tissue-Resident Memory Transcriptional Profile
Cited by: 45
Author(s): Tyler Landrith, Suhas Sureshchandra, Andrea Rivera, Jessica Jang, Maham Rais, Meera G. Nair, Ilhem Messaoudi, Emma H. Wilson
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-32792-6

Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics
Cited by: 16
Author(s): Martin Jacobsen, Robert J. Beynon, Lee A. Gethings, Amy J. Claydon, James Langridge, Johannes P.C. Vissers, Alistair J. P. Brown, Dean E. Hammond
Software Mentions: 3
Published: about 6 years ago

10.1001/jamanetworkopen.2019.6362

Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome
Cited by: 10
Author(s): Giovanna L. Pozuelos, Meenakshi S. Kagda, Suzaynn F. Schick, Thomas Girke, David C. Volz, Prue Talbot
Software Mentions: 2
Published: over 5 years ago

10.1534/g3.120.401487

Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR
Cited by: 13
Author(s): Arash Akbarzadeh, Aimee Lee S. Houde, Ben J. G. Sutherland, Oliver P. Günther, Kristina M. Miller
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-41234-w

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis
Cited by: 49
Author(s): Emily J. Blair, Titouan Bonnot, Maureen Hummel, Erika Hay, Jill M. Marzolino, Ivan A. Quijada, Dawn H. Nagel
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.01251-20

Invertases in Phytophthora infestans Localize to Haustoria and Are Programmed for Infection-Specific Expression
Cited by: 4
Author(s): Meenakshi S. Kagda, Domingo Martínez‐Soto, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.714817

Transcriptional Analysis of Infection With Early or Late Isolates From the 2013–2016 West Africa Ebola Virus Epidemic Does Not Suggest Attenuated Pathogenicity as a Result of Genetic Variation
Cited by: 2
Author(s): Kevin J. Maroney, Amanda N. Pinski, Andrea Marzi, Ilhem Messaoudi
Software Mentions: 1
Published: about 3 years ago

Ecosyste.ms: Papers

Projects: bioconductor: systemPipeR

Papers Mentioning systemPipeR 27