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: zinbwave

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

Zero-Inflated Negative Binomial Model for RNA-Seq Data
1 version
Latest release: 12 months ago
6 dependent packages
66,590 downloads total

Papers Mentioning zinbwave 12

10.1371/journal.pcbi.1006361

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: about 6 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: about 4 years ago

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.12688/f1000research.12122.1

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Cited by: 14
Author(s): Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 12
Published: about 7 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: over 3 years ago

10.1186/s12864-019-5926-4

lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA
Cited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-018-4772-0

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
Cited by: 1,344
Author(s): Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.43696

Complementary networks of cortical somatostatin interneurons enforce layer specific control
Cited by: 82
Author(s): Alexander Naka, Julia Veit, Ben Shababo, Rebecca K. Chance, Davide Risso, David Stafford, Benjamin Snyder, Andrew Egladyous, Desiree Chu, Savitha Sridharan, Daniel P. Mossing, Liam Paninski, John Ngai, Hillel Adesnik
Software Mentions: 7
Published: over 5 years ago

10.15252/embj.2020107100

<i>De novo</i> DNA methylation controls neuronal maturation during adult hippocampal neurogenesis
Cited by: 17
Author(s): Sara Zocher, Rupert W. Overall, Gabriel Berdugo-Vega, Nicole Rund, Anne Karasinsky, Vijay S. Adusumilli, Christina Steinhauer, Sina Scheibenstock, Kristian Händler, Joachim L. Schultze, Federico Calegari, Gerd Kempermann
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-021-02341-y

PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data
Cited by: 22
Author(s): Dongyuan Song, Jingyi Jessica Li
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pbio.3000711

Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression
Cited by: 49
Author(s): Juliana M. Sá, Matthew Cannon, Ramoncito L. Caleon, Thomas E. Wellems, David Serre
Software Mentions: 4
Published: over 4 years ago

10.1080/20002297.2019.1653124

Sex-specific differences in the salivary microbiome of caries-active children
Cited by: 24
Author(s): Stephanie Ortiz, Elisa Herrman, Claudia Lyashenko, Anne Purcell, Kareem Raslan, Brandon Khor, Michael Snow, Anna Forsyth, Dong‐Hee Choi, Tom Maier, Curtis A. Machida
Software Mentions: 2
Published: almost 6 years ago