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/s13059-021-02363-6

https://doi.org/10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways

Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Published: over 3 years ago

Software Mentions 9

bioconductor: CATALYST
Cytometry dATa anALYSis Tools
Papers that mentioned: 37
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: diffcyt
Differential discovery in high-dimensional cytometry via high-resolution clustering
Papers that mentioned: 18
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
Papers that mentioned: 177
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: projectR
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Papers that mentioned: 2
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Papers that mentioned: 276
pypi: salmon
A simple metric collector with alerts.
Papers that mentioned: 36