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: 10.3390/cancers13122903

https://doi.org/10.3390/cancers13122903

Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma

Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Published: over 3 years ago

Software Mentions 11

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
bioconductor: AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Papers that mentioned: 45
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: oligo
Preprocessing tools for oligonucleotide arrays
Papers that mentioned: 204
bioconductor: singscore
Rank-based single-sample gene set scoring method
Papers that mentioned: 13
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Papers that mentioned: 276
cran: Seurat
Tools for Single Cell Genomics
Papers that mentioned: 1,512
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: Harmony
Harmony Programming Language
Papers that mentioned: 504
pypi: oligo
UNOFFICIAL Python client for i-DE
Papers that mentioned: 204