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/s12859-017-1770-1

https://doi.org/10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction

Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Published: over 7 years ago

Software Mentions 10

bioconductor: ChIPQC
Quality metrics for ChIPseq data
Papers that mentioned: 15
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: RUVSeq
Remove Unwanted Variation from RNA-Seq Data
Papers that mentioned: 91
cran: randomForest
Breiman and Cutler's Random Forests for Classification and Regression
Papers that mentioned: 1,447
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysis
Papers that mentioned: 43
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
pypi: house
A lib to persist blobs by their sha256
Papers that mentioned: 960
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203