bioconductor: BSgenome | Projects

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1186/s12859-015-0683-0

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Cited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: about 9 years ago

10.1186/s12864-018-4559-3

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 6 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: almost 4 years ago

10.1038/srep26929

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
Cited by: 43
Author(s): Fábio Pértille, Carlos Guerrero-Bosagna, Vinícius da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: over 13 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: almost 7 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

10.1038/s41598-017-07880-8

Global mapping of miRNA-target interactions in cattle (Bos taurus)
Cited by: 19
Author(s): Troels K. H. Scheel, Michael J. Moore, Joseph M. Luna, Eiko Nishiuchi, John Fak, Robert B. Darnell, Charles M. Rice
Software Mentions: 9
Published: about 7 years ago

10.3389/fphys.2020.624677

Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
Cited by: 8
Author(s): Rui Fu, Austin E. Gillen, Katharine R. Grabek, Kent Riemondy, L. Elaine Epperson, Carlos D. Bustamante, Jay R. Hesselberth, Sandra L. Martin
Software Mentions: 9
Published: over 3 years ago

10.1038/srep46112

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing
Cited by: 31
Author(s): José de Ribamar da Silva Nunes, Shikai Liu, Fábio Pértille, Caio Augusto Perazza, Priscilla Marqui Schmidt Villela, Vera Maria Fonseca de Almeida-Val, Alexandre Wagner Silva Hilsdorf, Zhanjiang Liu, Luiz Lehmann Coutinho
Software Mentions: 9
Published: over 7 years ago

10.7150/jgen.41196

crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications
Cited by: 2
Author(s): Dylan Beeber, Frédéric J. J. Chain
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12864-017-3746-y

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
Cited by: 29
Author(s): Lihua Julie Zhu, Michael C. Lawrence, Ankit Gupta, Hervé Pagès, Alper Küçükural, Manuel Garber, Scot A. Wolfe
Software Mentions: 8
Published: over 7 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: almost 8 years ago

10.1186/1471-2164-15-284

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
Cited by: 743
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler
Software Mentions: 8
Published: almost 11 years ago

10.1186/1471-2164-14-S5-S9

Detection and classification of peaks in 5' cap RNA sequencing data
Cited by: 4
Author(s): Dario Strbenac, Nicola J. Armstrong, Jean Yee Hwa Yang
Software Mentions: 8
Published: about 11 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: over 13 years ago

10.1371/journal.pcbi.1006169

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Cited by: 115
Author(s): Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J N Groen, Thomas H. Gillingwater, Gabriella Viero
Software Mentions: 7
Published: about 6 years ago

10.1186/s13072-018-0205-1

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
Cited by: 243
Author(s): Dafni Anastasiadi, Anna Esteve‐Codina, Francesc Piferrer
Software Mentions: 6
Published: over 6 years ago

10.1186/s13073-017-0511-4

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells
Cited by: 6
Author(s): Snehangshu Kundu, Muhammad Akhtar-Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R. Wiśniewski, Per Artursson, Liqun He, Mats Hellström, Tobias Sjöblom
Software Mentions: 6
Published: almost 7 years ago

10.3390/ijms22179337

Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients
Cited by: 3
Author(s): Alicja Pacholewska, Christina Grimm, Carmen D. Herling, Matthias Lienhard, Anja Königs, Bernd Timmermann, Janine Altmüller, Oliver Mücke, Hans Christian Reinhardt, Christoph Plass, Ralf Herwig, Michael Hallek, Michal R. Schweiger
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pgen.1002389

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
Cited by: 340
Author(s): Michael J. Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B. Epstein, B Bernstein, Thomas Lengauer, Andreas Gnirke, Alexander Meissner
Software Mentions: 5
Published: almost 13 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: over 7 years ago

10.1083/jcb.201711097

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1
Cited by: 3
Author(s): Christoph Schiklenk, Boryana Petrova, Marc Kschonsak, Markus Hassler, Carlo Klein, Toby J. Gibson, Christian H. Haering
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-57476-y

Latency and interval therapy affect the evolution in metastatic colorectal cancer
Cited by: 5
Author(s): Hamid Nikbakht, Selin Jessa, Mahadeo A. Sukhai, Madeleine Arseneault, Tong Zhang, Louis Létourneau, Mariam Thomas, Mathieu Bourgey, Michael H. A. Roehrl, Robert Eveleigh, Eric X. Chen, Monika K. Krzyzanowska, Malcolm J. Moore, Amanda Giesler, Celeste Yu, Philippe L. Bedard, Suzanne Kamel‐Reid, Jacek Majewski, Lillian L. Siu, Yasser Riazalhosseini, Donna M. Graham
Software Mentions: 4
Published: over 4 years ago

10.1186/s12861-015-0085-6

Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Cited by: 6
Author(s): Christian Larney, Timothy L. Bailey, Peter Koopman
Software Mentions: 4
Published: about 9 years ago

10.1093/bioinformatics/btv470

<i>motifbreakR</i>: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
Cited by: 179
Author(s): Simon Coetzee, Gerhard A. Coetzee, Dennis J. Hazelett
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pcbi.1006451

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals
Cited by: 9
Author(s): Iksoo Huh, Isabel Mendizabal, Taesung Park, Soojin V. Yi
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0108424

CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems
Cited by: 156
Author(s): Lihua Julie Zhu, Benjamin Holmes, Neil Aronin, Michael Brodsky
Software Mentions: 4
Published: about 10 years ago

10.3389/fgene.2016.00075

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions
Cited by: 35
Author(s): Valerio Bianchi, Arnaud Céol, Alessandro G. E. Ogier, Stefano de Pretis, Eugenia Galeota, Kamal Kishore, Pranami Bora, Ottavio Croci, Stefano Campaner, Bruno Amati, Marco J. Morelli, Mattia Pelizzola
Software Mentions: 4
Published: over 8 years ago

10.3389/fnmol.2020.00057

Sequences of Reverse Transcribed Brain DNA Are Modified by Learning
Cited by: 2
Author(s): Antonio Giuditta, Joyce Casalino
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-019-1918-6

Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes
Cited by: 4
Author(s): Maroun Bou Sleiman, Michael Frochaux, Tommaso Andreani, Dani Osman, Roderic Guigó, Bart Deplancke
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.23517

Treatment-associated <i>TP53</i> DNA-binding domain missense mutations in the pathogenesis of secondary gliosarcoma
Cited by: 20
Author(s): Margaret Pain, Huaien Wang, Eunjee Lee, Maya Strahl, Wissam Hamou, Robert Sebra, Jun Zhu, Raymund L. Yong
Software Mentions: 3
Published: almost 7 years ago

10.1186/gb-2014-15-6-r86

IVT-seq reveals extreme bias in RNA sequencing
Cited by: 135
Author(s): Nicholas F. Lahens, İbrahim Halil Kavaklı, Ray Zhang, Katharina E. Hayer, Michael B. Black, Hannah Dueck, Angel Pizarro, Junhyong Kim, Rafael A. Irizarry, Russell S. Thomas, Gregory R. Grant, John B. Hogenesch
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-39633-0

Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
Cited by: 24
Author(s): Marco Cavalli, Nicholas Baltzer, Husen M. Umer, Jan Grau, Ioana Lemnian, Gang Pan, Ola Wallerman, Rapolas Spalinskas, Pelin Sahlén, Ivo Große, Jan Komorowski, Claes Wadelius
Software Mentions: 3
Published: over 5 years ago

10.12688/wellcomeopenres.10004.1

SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics
Cited by: 120
Author(s): Przemyslaw Stempor, Julie Ahringer
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep32196

RETRACTED ARTICLE: PPP1, a plant-specific regulator of transcription controls Arabidopsis development and PIN expression
Cited by: 5
Author(s): René Benjamins, Elke Barbez, Martina Ortbauer, Inez Terpstra, Doris Lucyshyn, Jeanette Moulinier-Anzola, Muhammad Asaf Khan, Johannes Leitner, Nenad Malenica, Haroon Butt, Barbara Korbei, Ben Scheres, Jürgen Kleine‐Vehn, Christian Luschnig
Software Mentions: 2
Published: about 8 years ago

10.18632/aging.103203

NAC1 attenuates BCL6 negative autoregulation and functions as a BCL6 coactivator of FOXQ1 transcription in cancer cells
Cited by: 5
Author(s): Min Gao, Alice Laschuk Herlinger, Ren‐Chin Wu, Tian Li Wang, Ie Ming Shih, Beihua Kong, Letícia Batista Azevedo Rangel, Jin Ming Yang
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.02105

Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells
Cited by: 74
Author(s): Nicolas Descostes, Martin Heidemann, Lionel Spinelli, Roland Schüller, Muhammad Ahmad Maqbool, Romain Fenouil, Frank‐Thomas Koch, Charlène Innocenti, Marta Gut, Dirk Eick, Jean-Christophe Andrau
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1007968

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats
Cited by: 4
Author(s): Hui Yu, Shilin Zhao, Scott A. Ness, Huining Kang, Quanhu Sheng, David C. Samuels, Olufunmilola Oyebamiji, Zhao Yan, Yan Guo
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-30330-y

Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
Cited by: 33
Author(s): Paola Orsini, Crescenzio Francesco Minervini, Cosimo Cumbo, Luisa Anelli, Antonella Zagaria, Angela Minervini, Nicoletta Coccaro, Giuseppina Tota, Paola Casieri, Luciana Impera, Elisa Parciante, Claudia Brunetti, Annamaria Giordano, Giorgina Specchia, Francesco Albano
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-27676-8

LSD1-ERRα complex requires NRF1 to positively regulate transcription and cell invasion
Cited by: 10
Author(s): Ling Zhang, Julie Carnesecchi, Catherine Cerutti, Violaine Tribollet, Séverine Périan, Christelle Forcet, Jiemin Wong, Jean‐Marc Vanacker
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2164-15-669

Genome-wide association study combined with biological context can reveal more disease-related SNPs altering microRNA target seed sites
Cited by: 10
Author(s): Di Wu, Gang Yang, Lifang Zhang, Jiwei Xue, Zhining Wen, Menglong Li
Software Mentions: 1
Published: about 10 years ago

10.18632/oncotarget.11773

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes
Cited by: 34
Author(s): Carl Mårten Lindqvist, Anders Lundmark, Jessica Nordlund, Eva Freyhult, Diana Ekman, Jonas Carlsson Almlöf, Amanda Raine, Elin Övernäs, Jonas Abrahamsson, Britt Marie Frost, Dan Grandér, Mats Heyman, Josefine Palle, Erik Forestier, Gudmar Lönnerholm, Eva Berglund, Ann Christine Syvänen
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-020-6526-z

Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows
Cited by: 27
Author(s): Zhihua Ju, Qiang Jiang, Jinpeng Wang, Xiuge Wang, Chunhong Yang, Yan Sun, Yaran Zhang, Changfa Wang, Yaping Gao, Xiaochao Wei, Minghai Hou, Jinming Huang
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: BSgenome

Papers Mentioning BSgenome 47