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/s13059-021-02337-8
https://doi.org/10.1186/s13059-021-02337-8
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Published: about 3 years ago
Software Mentions 10
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
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
pypi: MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.Papers that mentioned: 306