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An open API service providing mapping between scientific papers and software projects that are mentioned in them.

Papers: 10.1128/mBio.00399-21

https://doi.org/10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System

Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Published: about 4 years ago

Software Mentions 9

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
Very Likely Science (83)
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
bioconductor: ReactomePA
Reactome Pathway Analysis
Papers that mentioned: 171
Very Likely Science (100)
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
Very Likely Science (100)
cran: dplyr
A Grammar of Data Manipulation
Papers that mentioned: 1,213
Very Likely Science (100)
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
Very Likely Science (100)
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
Very Likely Science (75)
pypi: CellProfiler
An open-source application for biological image analysis
Papers that mentioned: 1,504
Very Likely Science (100)
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
Very Likely Science (100)