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/s40478-020-0880-6

https://doi.org/10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states

Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Published: over 4 years ago

Software Mentions 14

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
bioconductor: monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Papers that mentioned: 60
bioconductor: SC3
Single-Cell Consensus Clustering
Papers that mentioned: 71
bioconductor: scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
Papers that mentioned: 79
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
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: MEGENA
Multiscale Clustering of Geometrical Network
Papers that mentioned: 23
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893
pypi: monocle
An async programming framework with a blocking look-alike syntax
Papers that mentioned: 60
pypi: sc3
SuperCollider library for Python
Papers that mentioned: 2