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Papers: 10.1093/bioinformatics/bty947

https://doi.org/10.1093/bioinformatics/bty947

SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data

Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Published: over 7 years ago

Software Mentions 18

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
Very Likely Science (83)
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
bioconductor: ExpressionAtlas
Download datasets from EMBL-EBI Expression Atlas
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: genefilter
genefilter: methods for filtering genes from high-throughput experiments
Papers that mentioned: 142
Very Likely Science (75)
bioconductor: goseq
Gene Ontology analyser for RNA-seq and other length biased data
Papers that mentioned: 132
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: RankProd
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Papers that mentioned: 213
Very Likely Science (100)
bioconductor: RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
Papers that mentioned: 55
Very Likely Science (90)
bioconductor: RGalaxy
Papers that mentioned: 1
Unlikely Science (0)
bioconductor: sva
Surrogate Variable Analysis
Papers that mentioned: 511
Very Likely Science (100)
cran: dbscan
Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms
Papers that mentioned: 49
Very Likely Science (100)
cran: enrichR
Provides an R Interface to 'Enrichr'
Papers that mentioned: 60
Likely Science (58)
cran: GeoDE
A geometrical Approach to Differential expression and gene-set enrichment
Papers that mentioned: 1
Very Likely Science (85)
cran: plotly
Create Interactive Web Graphics via 'plotly.js'
Papers that mentioned: 163
Very Likely Science (100)
cran: Rtsne
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Papers that mentioned: 255
Very Likely Science (100)
pypi: dbscan
Theoretically efficient and practical parallel DBSCAN
Papers that mentioned: 49
Very Likely Science (100)
pypi: Expression
Practical functional programming for Python 3.9+
Papers that mentioned: 200
Very Likely Science (65)
pypi: plotly
An open-source, interactive data visualization library for Python
Papers that mentioned: 163
Very Likely Science (90)