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: 10.1093/gigascience/giy123

https://doi.org/10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix

Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Published: about 6 years ago

Software Mentions 15

bioconductor: bsseq
Analyze, manage and store bisulfite sequencing data
Papers that mentioned: 38
bioconductor: chipseq
chipseq: A package for analyzing chipseq data
Papers that mentioned: 9
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: GenomicRanges
Representation and manipulation of genomic intervals
Papers that mentioned: 323
bioconductor: iSEE
Interactive SummarizedExperiment Explorer
Papers that mentioned: 13
bioconductor: netSmooth
Network smoothing for scRNAseq
Papers that mentioned: 8
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
bioconductor: SingleCellExperiment
S4 Classes for Single Cell Data
Papers that mentioned: 36
bioconductor: zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Papers that mentioned: 12
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: diffoscope
in-depth comparison of files, archives, and directories
Papers that mentioned: 1
pypi: guix
Make faster cross platform GUI
Papers that mentioned: 1
pypi: loompy
Work with Loom files for single-cell RNA-seq data
Papers that mentioned: 1
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203