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 Research
Cited 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 discovery
Cited 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 data
Cited 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 Heart
Cited 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: almost 6 years ago

10.1186/s13059-021-02313-2

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities
Cited 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 data
Cited 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 data
Cited 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 tumors
Cited by: 32
Author(s): Jiasheng Xu, Kaili Liao, Yang Xi, Chengfeng Wu, Wei Wu, Shuwen Han
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2020.00662

Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies
Cited 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 analysis
Cited 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 studies
Cited 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 Pancreas
Cited 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 challenges
Cited 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 modeling
Cited by: 22
Author(s): Alma Anderson, Joakim Lundeberg
Software Mentions: 1
Published: over 3 years ago