cran: Signac | Projects | Ecosyste.ms: Papers

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

10.1038/s41597-020-00638-4

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance
Cited by: 117
Author(s): Sebastiaan P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper Welzel Andersen, Francisco Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro, Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola Marzari, Boris Kozinsky, Giovanni Pizzi
Software Mentions: 9
Published: about 4 years ago

10.3389/fncel.2021.648570

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
Cited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
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

10.1002/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

10.7554/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: over 3 years ago

10.3390/v13071197

Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal
Cited by: 3
Author(s): Suhui Zhao, Athe Tsibris
Software Mentions: 6
Published: over 3 years ago

10.1172/jci.insight.144294

The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling
Cited by: 20
Author(s): Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret Gruca, Jonathan Cardwell, Tsukasa Okamoto, Hong Wei Chu, Xiaomeng Hou, Olivier Poirion, Justin Buchanan, Sebastian Preißl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana V. Yang, David A. Schwartz, Anthony N. Gerber
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-021-02505-w

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Cited by: 23
Author(s): Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Yahan Liang, B Wold, A Mortazavi
Software Mentions: 5
Published: about 3 years ago

10.1016/j.jtos.2021.03.010

A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells
Cited by: 84
Author(s): Joseph Collin, Rachel Queen, Darin Zerti, Sanja Bojić, Birthe Dorgau, Nicky Moyse, Marina Moya Molina, Chunbo Yang, Sunanda Dey, Gary Reynolds, Rafiqul Hussain, Jonathan Coxhead, Steven Lisgo, Deborah J. Henderson, Agatha Joseph, Paul Rooney, Saurabh Ghosh, Lucy Clarke, Che J. Connon, Muzlifah Haniffa, Francisco C Figueiredo, Lyle Armstrong, Majlinda Lako
Software Mentions: 5
Published: over 3 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

10.3389/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: over 3 years ago

10.1186/s13072-021-00418-3

Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation
Cited by: 5
Author(s): Yujuan Gui, Kamil Grzyb, Mélanie Thomas, Jochen Ohnmacht, Pierre Garcia, Manuel Buttini, Alexander Skupin, Thomas Sauter, Lasse Sinkkonen
Software Mentions: 4
Published: about 3 years ago

10.1038/s12276-020-00499-2

Single-cell sequencing techniques from individual to multiomics analyses
Cited by: 116
Author(s): Yukie Kashima, Yoshitaka Sakamoto, Keiya Kaneko, Masahide Seki, Yutaka Suzuki, Ayako Suzuki
Software Mentions: 4
Published: about 4 years ago

10.1073/pnas.2023070118

BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
Cited by: 55
Author(s): Kevin Wu, Kathryn E. Yost, Howard Y. Chang, James Zou
Software Mentions: 3
Published: over 3 years ago

10.3389/fcell.2021.645276

Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution
Cited by: 9
Author(s): Ernesto Marín-Sedeño, Xabier Martínez de Morentin, José M. Pérez‐Pomares, David Green, Adrián Ruiz‐Villalba
Software Mentions: 3
Published: over 3 years ago

10.1177/2041669518788582

Area Dominates Edge in Pointillistic Colour
Cited by: 5
Author(s): Jan J. Koenderink, Andrea van Doorn, Karl R. Gegenfurtner
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-021-02469-x

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data
Cited by: 23
Author(s): Asa Thibodeau, Alper Eroğlu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marcheş, Daniel N. Conrad, George A. Kuchel, Zev J. Gartner, Jacques Banchereau, Michael L. Stitzel, A. Ercüment Çiçek, Duygu Ucar
Software Mentions: 2
Published: about 3 years ago

10.1186/s40246-021-00338-z

Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome
Cited by: 1
Author(s): Xiaofen Qiu, Haiyan Yu, Hongwei Wu, Zongxiang Hu, Jun Zhou, Lin Hua, Wen Xue, Wanxia Cai, Jiejing Chen, Yan Qiang, Weier Dai, Ming Yang, Donge Tang, Yong Dai
Software Mentions: 2
Published: over 3 years ago

10.1167/iovs.62.6.18

Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing—Opening Pathways to New Therapeutic Strategies?
Cited by: 11
Author(s): Joseph Collin, Rachel Queen, Darin Zerti, David Steel, Claire Bowen, Manoj Parulekar, Majlinda Lako
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2021.702636

Exploiting Single-Cell Tools in Gene and Cell Therapy
Cited by: 15
Author(s): Daniel Bode, Alyssa Cull, Juan Rubio‐Lara, David G. Kent
Software Mentions: 2
Published: over 3 years ago

10.3390/jdb8040031

Transcriptional Trajectories in Mouse Limb Buds Reveal the Transition from Anterior-Posterior to Proximal-Distal Patterning at Early Limb Bud Stage
Cited by: 9
Author(s): Inès Desanlis, Rachel Paul, Marie Kmita
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2021.697412

Applications of Single-Cell Omics in Tumor Immunology
Cited by: 21
Author(s): Junwei Liu, Saisi Qu, Tongtong Zhang, Yufei Gao, Hongyu Shi, Kaichen Song, Wei Chen, Weiwei Yin
Software Mentions: 1
Published: over 3 years ago

Ecosyste.ms: Papers

Projects: cran: Signac

Papers Mentioning Signac 24