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.
bioconductor projects 1,374
bioconductor: MOGAMUN
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological NetworksPapers that mentioned: 3
bioconductor: paxtoolsr
Access Pathways from Multiple Databases Through BioPAX and Pathway CommonsPapers that mentioned: 3
bioconductor: switchBox
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithmPapers that mentioned: 3
bioconductor: SummarizedBenchmark
Classes and methods for performing benchmark comparisonsPapers that mentioned: 3
bioconductor: iterativeBMA
The Iterative Bayesian Model Averaging (BMA) algorithmPapers that mentioned: 3
bioconductor: beadarraySNP
Normalization and reporting of Illumina SNP bead arraysPapers that mentioned: 3
bioconductor: SLGI
Papers that mentioned: 3bioconductor: IdeoViz
Plots data (continuous/discrete) along chromosomal ideogramPapers that mentioned: 3
bioconductor: flowVS
Variance stabilization in flow cytometry (and microarrays)Papers that mentioned: 3
bioconductor: compartmap
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seqPapers that mentioned: 3
bioconductor: arrayMvout
multivariate outlier detection for expression array QAPapers that mentioned: 3
bioconductor: DEqMS
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.Papers that mentioned: 3
bioconductor: rcellminer
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell LinesPapers that mentioned: 3
bioconductor: imageHTS
Analysis of high-throughput microscopy-based screensPapers that mentioned: 3
bioconductor: SubCellBarCode
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteomePapers that mentioned: 3
bioconductor: annotationTools
Annotate microarrays and perform cross-species gene expression analyses using flat file databasesPapers that mentioned: 3
bioconductor: MPFE
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing dataPapers that mentioned: 3
bioconductor: chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq DataPapers that mentioned: 3
bioconductor: myvariant
Accesses MyVariant.info variant query and annotation servicesPapers that mentioned: 3
bioconductor: scClassify
scClassify: single-cell Hierarchical ClassificationPapers that mentioned: 3
bioconductor: gep2pep
Creation and Analysis of Pathway Expression Profiles (PEPs)Papers that mentioned: 3
bioconductor: RIVER
R package for RIVER (RNA-Informed Variant Effect on Regulation)Papers that mentioned: 3
bioconductor: flowCHIC
Analyze flow cytometric data using histogram informationPapers that mentioned: 3
bioconductor: Nebulosa
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density EstimationPapers that mentioned: 3
bioconductor: VanillaICE
A Hidden Markov Model for high throughput genotyping arraysPapers that mentioned: 3
bioconductor: LPE
Methods for analyzing microarray data using Local Pooled Error (LPE) methodPapers that mentioned: 3
bioconductor: MetCirc
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics dataPapers that mentioned: 3
bioconductor: flowPloidy
Analyze flow cytometer data to determine sample ploidyPapers that mentioned: 3
bioconductor: caOmicsV
Papers that mentioned: 3bioconductor: TCGAbiolinksGUI
Papers that mentioned: 3bioconductor: DEsubs
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experimentsPapers that mentioned: 3
bioconductor: panp
Presence-Absence Calls from Negative Strand Matching ProbesetsPapers that mentioned: 3
bioconductor: diffGeneAnalysis
Performs differential gene expression AnalysisPapers that mentioned: 3
bioconductor: lmdme
Linear Model decomposition for Designed Multivariate ExperimentsPapers that mentioned: 3
bioconductor: DNABarcodes
A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experimentsPapers that mentioned: 3
bioconductor: OncoSimulR
Forward Genetic Simulation of Cancer Progression with EpistasisPapers that mentioned: 3
bioconductor: affyPara
Papers that mentioned: 2bioconductor: ANCOMBC
Microbiome differential abudance and correlation analyses with bias correctionPapers that mentioned: 2
bioconductor: BiocSingular
Singular Value Decomposition for Bioconductor PackagesPapers that mentioned: 2
bioconductor: circRNAprofiler
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAsPapers that mentioned: 2
bioconductor: chromswitch
An R package to detect chromatin state switches from epigenomic dataPapers that mentioned: 2
bioconductor: ClusterSignificance
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted dataPapers that mentioned: 2
bioconductor: clustifyr
Classifier for Single-cell RNA-seq Using Cell ClustersPapers that mentioned: 2
bioconductor: CGHbase
CGHbase: Base functions and classes for arrayCGH data analysis.Papers that mentioned: 2
bioconductor: methylCC
Estimate the cell composition of whole blood in DNA methylation samplesPapers that mentioned: 2
bioconductor: mbkmeans
Mini-batch K-means Clustering for Single-Cell RNA-seqPapers that mentioned: 2
bioconductor: debrowser
Interactive Differential Expresion Analysis BrowserPapers that mentioned: 2
bioconductor: miRspongeR
Identification and analysis of miRNA sponge regulationPapers that mentioned: 2
bioconductor: MoonlightR
Identify oncogenes and tumor suppressor genes from omics dataPapers that mentioned: 2
bioconductor: DiscoRhythm
Interactive Workflow for Discovering Rhythmicity in Biological DataPapers that mentioned: 2
bioconductor: FindMyFriends
Papers that mentioned: 2bioconductor: FLAMES
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq dataPapers that mentioned: 2
bioconductor: NetPathMiner
NetPathMiner for Biological Network Construction, Path Mining and VisualizationPapers that mentioned: 2
bioconductor: GeneExpressionSignature
Gene Expression Signature based Similarity MetricPapers that mentioned: 2