bioconductor: AnnotationHub | Projects

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: over 4 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.12688/f1000research.12544.1

Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: about 7 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
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

10.1038/s41416-020-0887-6

UGT2B17 modifies drug response in chronic lymphocytic leukaemia
Cited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 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

10.1186/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

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-019-50485-6

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Cited by: 28
Author(s): Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia
Software Mentions: 7
Published: about 5 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: almost 6 years ago

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: over 3 years ago

10.1093/bioinformatics/btaa591

Epiviz File Server: Query, transform and interactively explore data from indexed genomic files
Cited by: 4
Author(s): Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Héctor Corrada Bravo
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0233372

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs
Cited by: 20
Author(s): Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli, Roberta Davoli
Software Mentions: 6
Published: over 4 years ago

10.1126/sciadv.abh0534

Cell-free DNA TAPS provides multimodal information for early cancer detection
Cited by: 36
Author(s): Paulina Siejka-Zielińska, Jingfei Cheng, Felix Jackson, Yibin Liu, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Luminita Puta, Misti McCain, Emma L. Culver, Noor Bekkali, Benjamin Schuster-Böckler, Pier Francesco Palamara, Derek A. Mann, Helen L. Reeves, Eleanor Barnes, Shivan Sivakumar, Chun-Xiao Song
Software Mentions: 5
Published: about 3 years ago

10.1186/s13148-019-0769-z

DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression
Cited by: 6
Author(s): Dana M. Lapato, Roxann Roberson‐Nay, Robert M. Kirkpatrick, Bradley T. Webb, Timothy P. York, Patricia A. Kinser
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-07228-z

Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model
Cited by: 6
Author(s): Annette M. McCoy, Ann M. Kemper, M. Boyce, M. P. Brown, Troy N. Trumble
Software Mentions: 5
Published: almost 4 years ago

10.1093/bioinformatics/btx099

DeepBlueR: large-scale epigenomic analysis in R
Cited by: 6
Author(s): Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Software Mentions: 5
Published: over 7 years ago

10.12688/f1000research.15433.1

Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets
Cited by: 5
Author(s): Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Héctor Corrada Bravo
Software Mentions: 5
Published: over 6 years ago

10.3389/fonc.2020.00444

Multi-Omics Integration Reveals a Competitive Endogenous RNAs Network for the Identification of Progression Biomarkers and the Stratification of Patients Diagnosed With Nephroblastoma
Cited by: 2
Author(s): Jingbo Wang, Yuan Wang, Han Liang, Mohamed Shahen, Chaofeng Hu, Furong Li
Software Mentions: 5
Published: over 4 years ago

10.3390/genes10110944

Dissecting the Regulatory Network of Leaf Premature Senescence in Maize (Zea mays L.) Using Transcriptome Analysis of ZmELS5 Mutant
Cited by: 12
Author(s): Mao Chai, Zhanyong Guo, Xia Shi, Yingbo Li, Jian Tang, Zhan‐Hui Zhang
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21041518

The Molecular Mechanism of Perillaldehyde Inducing Cell Death in Aspergillus flavus by Inhibiting Energy Metabolism Revealed by Transcriptome Sequencing
Cited by: 18
Author(s): Chao Pan, Yongxin Li, Kunlong Yang, Famous Erhunmwunsee, Yan Ma, Xiaona He, Qingru Geng, Man Liu, Jun Tian
Software Mentions: 4
Published: over 4 years ago

10.6026/97320630013025

Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data
Cited by: 1
Author(s): Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41597-020-00772-z

A gene expression atlas for different kinds of stress in the mouse brain
Cited by: 27
Author(s): Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Andrea Mele, Alberto Oliverio, Cecilia Mannironi, Arianna Rinaldi, Tiziana Castrignanò
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-018-4800-0

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits
Cited by: 20
Author(s): Min Wang, Tim Hancock, Amanda J. Chamberlain, Christy J. Vander Jagt, J.E. Pryce, Benjamin G. Cocks, Michael E. Goddard, Ben J. Hayes
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.01178

Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins
Cited by: 7
Author(s): Ronaldo da Silva Francisco, Cristina dos Santos Ferreira, Juan Carlo Santos e Silva, Douglas Terra Machado, Yasmmin Martins, Víctor Ramos, Gustavo Simões Carnivali, Anice Garcia, Enrique Medina‐Acosta
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2021.641756

Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete
Cited by: 0
Author(s): Andrew Hesketh, Giselda Bucca, Colin P. Smith, Hee‐Jeon Hong
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2019.00603

Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data
Cited by: 13
Author(s): Nie Tengkun, Dongdong Wang, Xiaoyan Ma, Yue Chen, Qin Chen
Software Mentions: 4
Published: over 5 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21249506

Maize microRNA166 Inactivation Confers Plant Development and Abiotic Stress Resistance
Cited by: 19
Author(s): Na Li, Tianxiao Yang, Zhanyong Guo, Qiusheng Wang, Mao Chai, Mingbo Wu, Xiaoqi Li, Weiya Li, Guangxian Li, Jihua Tang, Guiliang Tang, Zhanhui Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1042/BSR20202346

Identification of novel biomarkers involved in pulmonary arterial hypertension based on multiple-microarray analysis
Cited by: 18
Author(s): Yi Ma, Shu Shu Chen, Yan Feng, Huan Liang Wang
Software Mentions: 3
Published: about 4 years ago

10.1093/database/baab032

MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Cited by: 15
Author(s): Sébastien A. Choteau, Audrey Wagner, Philippe Pierre, Lionel Spinelli, Catherine Brun
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0154070

Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics
Cited by: 7
Author(s): Kathryn Gilroy, Anne Terry, Asif Naseer, Jeroen de Ridder, Amin Allahyar, Weiwei Wang, Eric J. Carpenter, Andrew L. Mason, Gane Ka‐Shu Wong, Ewan R. Cameron, Anna Kilbey, James C. Neil
Software Mentions: 2
Published: over 8 years ago

10.3390/life11080746

CXCR3 Expression and Genome-Wide 3′ Splice Site Selection in the TCGA Breast Cancer Cohort
Cited by: 1
Author(s): Lauren A Levesque, Scott William Roy, Nicole Salazar
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-5274-9

Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model
Cited by: 0
Author(s): Can Wang, Shihua Zhang
Software Mentions: 2
Published: almost 6 years ago

10.18632/aging.104056

Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer&#x2019;s disease
Cited by: 18
Author(s): Emma Coninx, Yap Ching Chew, Xiaojing Yang, Wei Guo, Amelie Coolkens, Sarah Baatout, Lieve Moons, Mieke Verslegers, Roel Quintens
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: AnnotationHub

Papers Mentioning AnnotationHub 39