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: 10.15252/msb.20188746

https://doi.org/10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial

Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Published: over 5 years ago

Software Mentions 20

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: iSEE
Interactive SummarizedExperiment Explorer
Papers that mentioned: 13
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data
Papers that mentioned: 1
bioconductor: MAST
Model-based Analysis of Single Cell Transcriptomics
Papers that mentioned: 668
bioconductor: scmap
A tool for unsupervised projection of single cell RNA-seq data
Papers that mentioned: 34
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
cran: DCA
Dynamic Correlation Analysis for High Dimensional Data
Papers that mentioned: 128
cran: SAVER
Single-Cell RNA-Seq Gene Expression Recovery
Papers that mentioned: 40
cran: Seurat
Tools for Single Cell Genomics
Papers that mentioned: 1,512
cran: SoupX
Single Cell mRNA Soup eXterminator
Papers that mentioned: 17
pypi: DCA
Count autoencoder for scRNA-seq denoising
Papers that mentioned: 128
pypi: ForceAtlas2
The ForceAtlas2 algorithm for Python (and NetworkX)
Papers that mentioned: 92
pypi: Harmony
Harmony Programming Language
Papers that mentioned: 504
pypi: MAST
MAterials Simulation Toolkit
Papers that mentioned: 668
pypi: PhenoGraph
Graph-based clustering for high-dimensional single-cell data
Papers that mentioned: 96
pypi: scanpy
Single-Cell Analysis in Python.
Papers that mentioned: 68
pypi: scLVM
scLVM
Papers that mentioned: 19
pypi: scmap
Assigns rgb colors to points on sphere.
Papers that mentioned: 34
pypi: voom
A python message bus that you can put 4 million volts through.
Papers that mentioned: 136