Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: SpatialDE
https://packages.ecosyste.ms/registries/pypi.org/packages/SpatialDE
Spatial and Temporal DE test
9 versions
Latest release: over 5 years ago
2 dependent packages
273 downloads last month
Papers Mentioning SpatialDE 14
10.3390/ijms22062822
A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer ResearchCited by: 6
Author(s): Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
Software Mentions: 16
Published: over 3 years ago
10.1136/jitc-2020-000705
SITC cancer immunotherapy resource document: a compass in the land of biomarker discoveryCited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: almost 4 years ago
10.1186/s13059-021-02286-2
Giotto: a toolbox for integrative analysis and visualization of spatial expression dataCited by: 290
Author(s): Ruben Dries, Qi Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao, Rani E. George, Nico Pierson, Long Cai, Guo‐Cheng Yuan
Software Mentions: 9
Published: over 3 years ago
10.3389/fcvm.2018.00167
Single Cell Gene Expression to Understand the Dynamic Architecture of the HeartCited by: 15
Author(s): Andrea Massaia, Patrícia Chaves, Sara Samari, Ricardo J. Miragaia, Kerstin B. Meyer, Sarah A. Teichmann, Michela Noseda
Software Mentions: 8
Published: about 6 years ago
10.1186/s13059-021-02313-2
Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalitiesCited by: 19
Author(s): Rohit Singh, Brian Hie, Ashwin Narayan, Bonnie Berger
Software Mentions: 5
Published: over 3 years ago
10.1186/s12915-020-00874-5
Automated identification of the mouse brain’s spatial compartments from in situ sequencing dataCited by: 16
Author(s): Gabriele Partel, Markus M. Hilscher, Milli Giorgia, Leslie Solorzano, Anna H. Klemm, Mats Nilsson, Carolina Wählby
Software Mentions: 4
Published: about 4 years ago
10.1093/bioinformatics/btaa198
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq dataCited by: 6
Author(s): Philipp Angerer, David Fischer, Fabian J. Theis, Antonio Scialdone, Carsten Marr
Software Mentions: 3
Published: over 4 years ago
10.1186/s12943-021-01392-w
Using single-cell sequencing technology to detect circulating tumor cells in solid tumorsCited by: 32
Author(s): Jiasheng Xu, Kaili Liao, Yang Xi, Chengfeng Wu, Wei Wu, Shuwen Han
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2020.00662
Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics TechnologiesCited by: 17
Author(s): Q. Xing, Nadia Omega Cipta, Kiyofumi Hamashima, Yih‐Cherng Liou, Cheng-Gee Koh, Yuin-Han Loh
Software Mentions: 2
Published: over 4 years ago
10.1186/s12859-021-04314-1
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysisCited by: 15
Author(s): Yang Xu, Rachel Patton McCord
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-021-02404-0
SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studiesCited by: 69
Author(s): Jiaqiang Zhu, Shuang Sun, Xiang Zhou
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-019-41951-2
Modeling Spatial Correlation of Transcripts with Application to Developing PancreasCited by: 7
Author(s): Ruishan Liu, Marco Mignardi, Robert C. Jones, Martin Enge, Seung K. Kim, Stephen R. Quake, James Zou
Software Mentions: 1
Published: over 5 years ago
10.1093/bfgp/elx029
The Human Cell Atlas: Technical approaches and challengesCited by: 34
Author(s): Chung-Chau Hon, Jay W. Shin, Piero Carninci, Michael J. T. Stubbington
Software Mentions: 1
Published: about 7 years ago
10.1093/bioinformatics/btab164
<i>sepal</i>: identifying transcript profiles with spatial patterns by diffusion-based modelingCited by: 22
Author(s): Alma Anderson, Joakim Lundeberg
Software Mentions: 1
Published: over 3 years ago