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/s12967-021-02936-w
https://doi.org/10.1186/s12967-021-02936-w
TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Published: over 3 years ago
Software Mentions 7
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
bioconductor: NOISeq
Exploratory analysis and differential expression for RNA-seq dataPapers that mentioned: 321
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisPapers that mentioned: 367
pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assaysPapers that mentioned: 3,071
pypi: kallisto
The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.Papers that mentioned: 307