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/s13059-019-1921-y

https://doi.org/10.1186/s13059-019-1921-y

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis

Cited by: 68
Author(s): Rui Yang, Sen Cheng, Nan Luo, Ranran Gao, Kezhuo Yu, Boxi Kang, Li Wang, Qiming Zhang, Fang Qiao, Lei Zhang, Chen Li, Aibin He, Xueda Hu, Jirun Peng, Xianwen Ren, Zemin Zhang
Published: almost 5 years ago

Software Mentions 8

bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
cran: Seurat
Tools for Single Cell Genomics
Papers that mentioned: 1,512
pypi: analysis
Source code analysis of Python programs
Papers that mentioned: 2,036
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893
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