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: compcodeR

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

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
2 versions
Latest release: about 1 year ago
19,616 downloads total

Papers Mentioning compcodeR 11

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago

10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: over 9 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: almost 7 years ago

10.1093/bioinformatics/btx631

Towards unified quality verification of synthetic count data with <i>countsimQC</i>
Cited by: 39
Author(s): Charlotte Soneson, Mark D. Robinson
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-015-0604-6

DGEclust: differential expression analysis of clustered count data
Cited by: 14
Author(s): Dimitrios V Vavoulis, Margherita Francescatto, Peter Heutink, Julian Gough
Software Mentions: 5
Published: over 9 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-021-07790-0

A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
Cited by: 4
Author(s): Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu, Guo‐Liang Tian
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers13071585

Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes
Cited by: 8
Author(s): Anna Privitera, Vincenza Barresi, D. F. Condorelli
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms20184652

Chromosomal Density of Cancer Up-Regulated Genes, Aberrant Enhancer Activity and Cancer Fitness Genes Are Associated with Transcriptional Cis-Effects of Broad Copy Number Gains in Colorectal Cancer
Cited by: 11
Author(s): D. F. Condorelli, Anna Privitera, Vincenza Barresi
Software Mentions: 1
Published: about 5 years ago