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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: about 6 years ago

Software Mentions 20

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
bioconductor: iSEE
Interactive SummarizedExperiment Explorer
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq data
Papers that mentioned: 1
Very Likely Science (100)
bioconductor: MAST
Model-based Analysis of Single Cell Transcriptomics
Papers that mentioned: 668
Very Likely Science (100)
bioconductor: scmap
A tool for unsupervised projection of single cell RNA-seq data
Papers that mentioned: 34
Very Likely Science (100)
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
Very Likely Science (100)
cran: DCA
Dynamic Correlation Analysis for High Dimensional Data
Papers that mentioned: 128
Very Likely Science (93)
cran: SAVER
Single-Cell RNA-Seq Gene Expression Recovery
Papers that mentioned: 40
Very Likely Science (100)
cran: Seurat
Tools for Single Cell Genomics
Papers that mentioned: 1,512
Very Likely Science (100)
cran: SoupX
Single Cell mRNA Soup eXterminator
Papers that mentioned: 17
Very Likely Science (100)
pypi: DCA
Count autoencoder for scRNA-seq denoising
Papers that mentioned: 128
Very Likely Science (100)
pypi: ForceAtlas2
The ForceAtlas2 algorithm for Python (and NetworkX)
Papers that mentioned: 92
Very Likely Science (75)
pypi: Harmony
Harmony Programming Language
Papers that mentioned: 504
Very Likely Science (65)
pypi: MAST
MAterials Simulation Toolkit
Papers that mentioned: 668
Very Likely Science (75)
pypi: PhenoGraph
Graph-based clustering for high-dimensional single-cell data
Papers that mentioned: 96
Very Likely Science (100)
pypi: scanpy
Single-Cell Analysis in Python.
Papers that mentioned: 68
Very Likely Science (100)
pypi: scLVM
scLVM
Papers that mentioned: 19
Very Likely Science (100)
pypi: scmap
Assigns rgb colors to points on sphere.
Papers that mentioned: 34
Very Likely Science (65)
pypi: voom
A python message bus that you can put 4 million volts through.
Papers that mentioned: 136
Likely Science (40)