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: cran: RaceID

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/RaceID

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
25 versions
Latest release: about 1 year ago
669 downloads last month

Papers Mentioning RaceID 25

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.1186/s12859-021-04210-8

Contrastive self-supervised clustering of scRNA-seq data
Cited by: 28
Author(s): Madalina Ciortan, Matthieu Defrance
Software Mentions: 13
Published: over 3 years ago

10.1093/gigascience/giaa102

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Cited by: 15
Author(s): Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, D. L. Clements, Fidel Ramírez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Léa Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning
Software Mentions: 12
Published: about 4 years ago

10.1093/bioinformatics/btz889

<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methods
Cited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: about 5 years ago

10.1186/s13059-016-0927-y

Design and computational analysis of single-cell RNA-sequencing experiments
Cited by: 409
Author(s): Rhonda Bacher, Christina Kendziorski
Software Mentions: 10
Published: over 8 years ago

10.1242/bio.052993

Site-1 protease ablation in the osterix-lineage in mice results in bone marrow neutrophilia and hematopoietic stem cell alterations
Cited by: 2
Author(s): Debabrata Patra, Joongho Kim, Qiang Zhang, Eric Tycksen, Linda J. Sandell
Software Mentions: 9
Published: over 4 years ago

10.3390/ijms22031399

DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
Cited by: 5
Author(s): Salim Ghannoum, Waldir Leoncio Netto, Damiano Fantini, Benjamin Ragan-Kelley, Amirabbas Parizadeh, Emma Jonasson, Anders Ståhlberg, Hesso Farhan, Alvaro Köhn‐Luque
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-017-1188-0

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
Cited by: 391
Author(s): Peijie Lin, Michael Troup, Joshua W. K. Ho
Software Mentions: 8
Published: over 7 years ago

10.3390/genes12020311

Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model
Cited by: 7
Author(s): Zhenqiu Liu
Software Mentions: 8
Published: almost 4 years ago

10.1093/bfgp/ely003

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system
Cited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: almost 7 years ago

10.1038/s42003-020-01364-8

Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse
Cited by: 22
Author(s): Tingzhen Mu, Liqin Xu, Yu Zhong, Xinyu Liu, Zhikun Zhao, Changyuan Huang, Xiaofeng Lan, Chengchen Lufei, Yi Zhou, Yixun Su, Luang Xu, Miaomiao Jiang, Hong Zhou, Xinxin Lin, Liang Wu, Siqi Peng, Shiping Liu, Susanne Brix, Michael Dean, N. Ray Dunn, Kenneth S. Zaret, Xin-Yuan Fu, Yong Hou
Software Mentions: 6
Published: about 4 years ago

10.1093/gigascience/giaa152

Tool recommender system in Galaxy using deep learning
Cited by: 7
Author(s): Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12885-021-08617-7

Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level
Cited by: 3
Author(s): Yan Zhang, Denan Zhang, Qingkang Meng, Ziqi Liu, Hongbo Xie, Lei Liu, Fei Xu, Xiujie Chen
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2019.00958

Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?
Cited by: 52
Author(s): Elisabetta Rossi, Rita Zamarchi
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2019.00371

High-Order Correlation Integration for Single-Cell or Bulk RNA-seq Data Analysis
Cited by: 9
Author(s): Hui Tang, Tao Zeng, Luonan Chen
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-016-1010-4

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index
Cited by: 229
Author(s): Lan Jiang, Huidong Chen, Luca Pinello, Guo‐Cheng Yuan
Software Mentions: 5
Published: over 8 years ago

10.3390/genes10080611

Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles
Cited by: 14
Author(s): Saurav Mallik, Zhongming Zhao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007040

PanoView: An iterative clustering method for single-cell RNA sequencing data
Cited by: 15
Author(s): Ming Hu, Dong Won Kim, Sheng Liu, Donald J. Zack, Seth Blackshaw, Jiang Qian
Software Mentions: 4
Published: over 5 years ago

10.26508/lsa.201900443

De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments
Cited by: 7
Author(s): Hyung Jun Woo, Boris Winterhoff, Timothy K. Starr, Constantin F. Aliferis, Jinhua Wang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-66848-3

Identification of cell types from single cell data using stable clustering
Cited by: 24
Author(s): Azam Peyvandipour, Adib Shafi, Nafiseh Saberian, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.1186/s41232-021-00170-x

Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition
Cited by: 18
Author(s): Satoi Nagasawa, Yukie Kashima, Ayako Suzuki, Yutaka Suzuki
Software Mentions: 3
Published: over 3 years ago