bioconductor: chromVAR | Projects

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago

10.15252/msb.20209438

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago

10.3389/fcell.2021.642724

Identification of Stemness-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Hongjun Guo, Siqiao Wang, Min Kyung Ju, Penghui Yan, Weiwei Sun, Zhenyu Li, Siyu Wu, Ruoyi Lin, Shuyuan Xian, Daoke Yang, Jun Wang, Zongqiang Huang
Software Mentions: 15
Published: over 3 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
Published: over 4 years ago

10.1111/jcmm.15705

Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 4 years ago

10.1016/j.cell.2021.04.048

Integrated analysis of multimodal single-cell data
Cited by: 4,423
Author(s): Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline Lee, Aaron J. Wilk, Charlotte A. Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, T.A. Stuart, Lamar M. Fleming, Bertrand Z. Yeung, Angela J. Rogers, Juliana McElrath, Catherine A. Blish, Raphaël Gottardo, Peter Smibert, Rahul Satija
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.49921

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices
Cited by: 21
Author(s): Claudia Racioppi, Keira A Wiechecki, Lionel Christiaen
Software Mentions: 11
Published: about 5 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: over 3 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago

10.1186/s13059-020-02034-y

APEC: an accesson-based method for single-cell chromatin accessibility analysis
Cited by: 11
Author(s): Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu
Software Mentions: 10
Published: over 4 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago

10.3389/fonc.2021.575425

Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Shiqiang Zhang, Wenzhong Zheng, Donggen Jiang, Haiyun Xiong, Guolong Liao, Xiangwei Yang, He Ma, Jun Li, Miaojuan Qiu, Binbin Li, Chunhui Sun, Jing Zhao, Liling Wang, Jun Pang
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.53278

GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm
Cited by: 25
Author(s): Arun Sharma, Lauren Wasson, Jon A. L. Willcox, Sarah U. Morton, Joshua M. Gorham, Daniel M. DeLaughter, Meraj Neyazi, Manuel Schmid, Radhika Agarwal, Min Young Jang, Christopher N. Toepfer, Tarsha Ward, Yuri Kim, Alexandre C. Pereira, Steven R. DePalma, Angela Tai, Seongwon Kim, David A. Conner, Daniel Bernstein, Bruce D. Gelb, Wendy K. Chung, Elizabeth Goldmuntz, George A. Porter, Martin Tristani‐Firouzi, Deepak Srivastava, Jonathan G. Seidman, Christine E. Seidman
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pcbi.1009064

coupleCoC+: An information-theoretic co-clustering-based transfer learning framework for the integrative analysis of single-cell genomic data
Cited by: 7
Author(s): Pengcheng Zeng, Zhixiang Lin
Software Mentions: 9
Published: over 3 years ago

10.1186/s40478-019-0851-y

Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas
Cited by: 12
Author(s): Ruslan Al‐Ali, Katharina Bauer, Jong‐Whi Park, Ruba Al-Abdulla, Valentina Fermi, Andreas von Deimling, Christel Herold‐Mende, Jan‐Philipp Mallm, Carl Herrmann, Wolfgang Wick, Şevin Turcan
Software Mentions: 9
Published: about 5 years ago

10.1186/s13059-020-02075-3

Single-cell ATAC-seq signal extraction and enhancement with SCATE
Cited by: 29
Author(s): Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji
Software Mentions: 8
Published: over 4 years ago

10.1002/ctm2.422

Single‐cell analyses reveal suppressive tumor microenvironment of human colorectal cancer
Cited by: 37
Author(s): Mei Yan, Weiwei Xiao, Hao Hu, Guan-Ming Lu, Lingdan Chen, Zhun Sun, Mengdie Lü, Wenhui Ma, Ting Jiang, Yuanhong Gao, LiRen Li, Gong Chen, Zifeng Wang, Hanjie Li, Duojiao Wu, Ping‐Hong Zhou, Qibin Leng, Guangshuai Jia
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.202010060

CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing
Cited by: 11
Author(s): Liang Fang, Guipeng Li, Zhiyuan Sun, Qionghua Zhu, Huanhuan Cui, Yunfei Li, Jingwen Zhang, Weizheng Liang, Wencheng Wei, Yuhui Hu, Wei Chen
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.64090

Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival
Cited by: 44
Author(s): Paul Guilhamon, Charles Chesnelong, Michelle Kushida, Ana Nikolić, Divya Singhal, Graham MacLeod, Seyed Ali Madani Tonekaboni, Florence M.G. Cavalli, Christopher Arlidge, Nishani Rajakulendran, Naghmeh Rastegar, Xiaoguang Hao, Rozina Hassam, Laura J. Smith, Heather Whetstone, Fiona J. Coutinho, Bettina Nadorp, Katrina Ellestad, H. Artee Luchman, Jennifer A. Chan, Molly S. Shoichet, Michael D. Taylor, Benjamin Haibe‐Kains, Samuel Weiss, Stéphane Angers, Marco Gallo, Peter B. Dirks, Mathieu Lupien
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.stem.2020.11.015

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Cited by: 152
Author(s): Anna Maria Ranzoni, Andrea Tangherloni, Ivan Berest, Simone G. Riva, Brynelle Myers, Paulina M. Strzelecka, Jiarui Xu, Elisa Panada, Irina Mohorianu, Judith B. Zaugg, Ana Cvejic
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.59388

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals
Cited by: 10
Author(s): Eric M. Sanford, Benjamin Emert, Allison Coté, Arjun Raj
Software Mentions: 6
Published: about 4 years ago

10.1186/s13059-019-1806-0

scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data
Cited by: 15
Author(s): Ruoxin Li, Gerald Quon
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-021-02339-6

Functional mapping of androgen receptor enhancer activity
Cited by: 15
Author(s): Chia Chi Flora Huang, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altıntaş, Mohammadali Saffarzadeh, Stéphane Le Bihan, Brian McConeghy, Bengul Gokbayrak, Felix Y. Feng, Martin Gleave, Andries M. Bergman, Colin C. Collins, Faraz Hach, Wilbert Zwart, Eldon Emberly, Nathan A. Lack
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.681206

LISA2: Learning Complex Single-Cell Trajectory and Expression Trends
Cited by: 1
Author(s): Yang Chen, Yuping Zhang, Kairong Li, Zhengqing Ouyang
Software Mentions: 5
Published: over 3 years ago

10.1007/s13238-020-00762-2

A human circulating immune cell landscape in aging and COVID-19
Cited by: 158
Author(s): Yingfeng Zheng, Xiuxing Liu, Wenqing Le, Lihui Xie, Li He, Wen Wen, Si Wang, Shuai Ma, Zhaofeng Huang, Jinguo Ye, Wen Shi, Yanxia Ye, Zunpeng Liu, Moshi Song, Weiqi Zhang, Jing‐Dong J. Han, Juan Carlos Izpisúa Belmonte, Chuan-Le Xiao, Jing Qu, Hongyang Wang, Guang‐Hui Liu, Wenru Su
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.633654

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition
Cited by: 11
Author(s): Xiaofang Xu, Dianhua Qiao, Chenyang Dong, Morgan Mann, Roberto P. Garofalo, Sündüz Keleş, Allan R. Brasier
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-020-02139-4

COCOA: coordinate covariation analysis of epigenetic heterogeneity
Cited by: 10
Author(s): John T. Lawson, Jason P. Smith, Stefan Bekiranov, Francine E. Garrett-Bakelman, Nathan C. Sheffield
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.625881

Epigenetic Landscapes of Single-Cell Chromatin Accessibility and Transcriptomic Immune Profiles of T Cells in COVID-19 Patients
Cited by: 28
Author(s): Shun Li, Bin Wu, Yun Ling, Mingquan Guo, Boyin Qin, Xu Ren, Chao Wang, Hua Yang, Lixiang Chen, Yixin Liao, Yang Liu, Xinjun Peng, Chunhua Xu, Zhenyan Wang, Yinzhong Shen, Jun Chen, Li Liu, Bowen Niu, Mengmin Zhu, Lingling Liu, Feng Li, Tongyu Zhu, Zhaoqin Zhu, Xiaohui Zhou, Hongzhou Lu
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-1932-8

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles
Cited by: 91
Author(s): Suoqin Jin, Lihua Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1038/s12276-020-0420-2

Single-cell multiomics: technologies and data analysis methods
Cited by: 239
Author(s): Jeongwoo Lee, Do Young Hyeon, Daehee Hwang
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02238-2

scMC learns biological variation through the alignment of multiple single-cell genomics datasets
Cited by: 418
Author(s): Lihua Zhang, Qing Nie
Software Mentions: 4
Published: almost 4 years ago

10.1172/jci.insight.141024

Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration
Cited by: 34
Author(s): Tianyi Chen, Seh–Hoon Oh, Simon Gregory, Xiling Shen, Anna Mae Diehl
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.60562

Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra
Cited by: 20
Author(s): Jack Cazet, Adrienne Cho, Celina E. Juliano
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-019-1854-5

Assessment of computational methods for the analysis of single-cell ATAC-seq data
Cited by: 197
Author(s): Huidong Chen, Caleb A. Lareau, Tommaso Andreani, Michael Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade‐Navarro, Jason D. Buenrostro, Luca Pinello
Software Mentions: 3
Published: about 5 years ago

10.1016/j.celrep.2020.107742

Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer
Cited by: 29
Author(s): John R. Christin, Chunhui Wang, Chi Yeh Chung, Yu Liu, Christopher Dravis, Wei Tang, Maja H. Oktay, Geoffrey M. Wahl, Wenjun Guo
Software Mentions: 3
Published: over 4 years ago

10.1073/pnas.2104758118

Dynamic chromatin regulatory landscape of human CAR T cell exhaustion
Cited by: 26
Author(s): David Gennert, Rachel C. Lynn, Jeff M. Granja, Evan W. Weber, Maxwell R. Mumbach, Yang Zhao, Zhana Duren, Elena Sotillo, William J. Greenleaf, Wing Hung Wong, Ansuman T. Satpathy, Crystal L. Mackall, Howard Y. Chang
Software Mentions: 3
Published: over 3 years ago

10.1093/bfgp/elx046

Mapping gene regulatory networks from single-cell omics data
Cited by: 165
Author(s): Mark Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-36057-0

Chromatin accessibility identifies diversity in mesenchymal stem cells from different tissue origins
Cited by: 27
Author(s): Yen-Ting Ho, Takashi Shimbo, Edward Wijaya, Yuya Ouchi, Eiichi Takaki, Ryusuke Yamamoto, Yasushi Kikuchi, Yasufumi Kaneda, Katsuto Tamai
Software Mentions: 3
Published: about 6 years ago

10.1161/CIRCRESAHA.120.316770

Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics
Cited by: 239
Author(s): Marie A.C. Depuydt, K.H.M. Prange, Lotte Slenders, Tiit Örd, D. Elbersen, Arjan Boltjes, Saskia C.A. de Jager, Folkert W. Asselbergs, Gert J. de Borst, Einari Aavik, Tapio Lönnberg, Esther Lutgens, Christopher K. Glass, Hester M. den Ruijter, Minna U. Kaikkonen, Ilze Bot, Bram Slütter, Sander W. van der Laan, Seppo Ylä‐Herttuala, Michal Mokrý, Johan Kuiper, Menno P.J. de Winther, Gérard Pasterkamp
Software Mentions: 3
Published: about 4 years ago

10.3389/fcell.2018.00028

Single Cell Multi-Omics Technology: Methodology and Application
Cited by: 114
Author(s): Youjin Hu, Qin An, Katherine M. Sheu, Brandon Trejo, Shuangshuang Fan, Ying Guo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-43021-z

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages
Cited by: 27
Author(s): Kazuhide Watanabe, Ye Liu, Shuhei Noguchi, Madeleine Murray, Jen-Chien Chang, Mami Kishima, Hajime Nishimura, Kosuke Hashimoto, Aki Minoda, Harukazu Suzuki
Software Mentions: 2
Published: over 5 years ago

10.1186/s43556-020-00009-w

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
Cited by: 26
Author(s): Shaoqian Ma, Yongyou Zhang
Software Mentions: 2
Published: about 4 years ago

10.1186/s13072-020-00377-1

Chromatin accessibility maps provide evidence of multilineage gene priming in hematopoietic stem cells
Cited by: 18
Author(s): Eric W. Martin, Jana Krietsch, Roman E. Reggiardo, Rebekah Sousae, Daniel H. Kim, Erik Forsberg
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.45105

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
Cited by: 83
Author(s): Jin Xu, Kevin A. Nuno, Ulrike M. Litzenburger, Yanyan Qi, M. Ryan Corces, Ravindra Majeti, Howard Y. Chang
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2018.00319

A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level
Cited by: 15
Author(s): Stanley Cai, Γεώργιος Γεωργακίλας, John L. Johnson, Golnaz Vahedi
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/btz141

Destin: toolkit for single-cell analysis of chromatin accessibility
Cited by: 26
Author(s): Eugene Urrutia, Li Chen, Haibo Zhou, Y. Jiang
Software Mentions: 1
Published: almost 6 years ago

Projects: bioconductor: chromVAR

Papers Mentioning chromVAR 46