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/s13059-020-02245-3

https://doi.org/10.1186/s13059-020-02245-3

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Cited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Published: almost 4 years ago

Software Mentions 10

bioconductor: CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Papers that mentioned: 27
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
cran: ggpubr
'ggplot2' Based Publication Ready Plots
Papers that mentioned: 856
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
cran: WGCNA
Weighted Correlation Network Analysis
Papers that mentioned: 3,479
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
pypi: deepTools
Useful tools for exploring deep sequencing data.
Papers that mentioned: 435
pypi: ggplot
ggplot for python
Papers that mentioned: 796
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203
pypi: stats
Calculator-style statistical functions
Papers that mentioned: 3,105