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/cells8111321

https://doi.org/10.3390/cells8111321

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets

Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Published: about 5 years ago

Software Mentions 15

bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Papers that mentioned: 161
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
bioconductor: ComplexHeatmap
Make Complex Heatmaps
Papers that mentioned: 565
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: EnrichedHeatmap
Making Enriched Heatmaps
Papers that mentioned: 12
bioconductor: GenomicRanges
Representation and manipulation of genomic intervals
Papers that mentioned: 323
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
bioconductor: goseq
Gene Ontology analyser for RNA-seq and other length biased data
Papers that mentioned: 132
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: rtracklayer
R interface to genome annotation files and the UCSC genome browser
Papers that mentioned: 107
cran: DGCA
Differential Gene Correlation Analysis
Papers that mentioned: 17
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: tidyverse
Easily Install and Load the 'Tidyverse'
Papers that mentioned: 1,023
cran: WGCNA
Weighted Correlation Network Analysis
Papers that mentioned: 3,479
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203