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: bioconductor: scDD

https://packages.ecosyste.ms/registries/bioconductor.org/packages/scDD

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
1 version
Latest release: about 1 year ago
1 dependent package
16,584 downloads total

Papers Mentioning scDD 16

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1002/1873-3468.12684

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/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: over 7 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 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

10.1186/s13073-020-00799-2

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities
Cited by: 20
Author(s): Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg, Olli Lohi, Merja Heinäniemi
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-017-16685-8

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
Cited by: 7
Author(s): Nadia Boufaied, Christopher Nash, Annie Rochette, Anthony K. Smith, Brigid Orr, O. Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 6
Published: about 7 years ago

10.3389/fnins.2021.591122

Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis
Cited by: 40
Author(s): Asif Adil, Vijay Kumar, Arif Tasleem Jan, M. Asger
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1922-x

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Cited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-07302-6

JOINT for large-scale single-cell RNA-sequencing analysis via soft-clustering and parallel computing
Cited by: 4
Author(s): Tao Cui, Tingting Wang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13293-020-00335-2

Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell types
Cited by: 18
Author(s): Tianyuan Lu, Jessica C. Mar
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-016-1077-y

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
Cited by: 210
Author(s): Keegan Korthauer, Li‐Fang Chu, Michael A. Newton, Yuan Li, James A. Thomson, Ron Stewart, Christina Kendziorski
Software Mentions: 3
Published: about 8 years ago

10.3390/genes8120368

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells
Cited by: 73
Author(s): Yuan Cao, Junjie Zhu, Peilin Jia, Zhongming Zhao
Software Mentions: 3
Published: about 7 years ago