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.

Papers: 10.1186/s12859-016-1457-z

https://doi.org/10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Published: almost 8 years ago

Software Mentions 13

bioconductor: baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
Papers that mentioned: 139
bioconductor: BitSeq
Papers that mentioned: 28
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq data
Papers that mentioned: 261
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
cran: NBPSeq
Negative Binomial Models for RNA-Sequencing Data
Papers that mentioned: 32
cran: SAM
Sparse Additive Modelling
Papers that mentioned: 4,566
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: cufflinks
Productivity Tools for Plotly + Pandas
Papers that mentioned: 415
pypi: custom
Custom self carry
Papers that mentioned: 1,363
pypi: wasabi
A lightweight console printing and formatting toolkit
Papers that mentioned: 3