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: immunoClust
immunoClust - Automated Pipeline for Population Detection in Flow CytometryPapers that mentioned: 2
bioconductor: INPower
An R package for computing the number of susceptibility SNPsPapers that mentioned: 2
bioconductor: InTAD
Search for correlation between epigenetic signals and gene expression in TADsPapers that mentioned: 2
bioconductor: IONiseR
Quality Assessment Tools for Oxford Nanopore MinION dataPapers that mentioned: 2
bioconductor: KCsmart
Multi sample aCGH analysis package using kernel convolutionPapers that mentioned: 2
bioconductor: LowMACA
LowMACA - Low frequency Mutation Analysis via Consensus AlignmentPapers that mentioned: 2
bioconductor: maigesPack
Functions to handle cDNA microarray data, including several methods of data analysisPapers that mentioned: 2
bioconductor: MetaVolcanoR
Gene Expression Meta-analysis Visualization ToolPapers that mentioned: 2
bioconductor: mfa
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcationsPapers that mentioned: 2
bioconductor: MinimumDistance
A Package for De Novo CNV Detection in Case-Parent TriosPapers that mentioned: 2
bioconductor: MMUPHin
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome StudiesPapers that mentioned: 2
bioconductor: msmsEDA
Exploratory Data Analysis of LC-MS/MS data by spectral countsPapers that mentioned: 2
bioconductor: multiClust
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome ProfilesPapers that mentioned: 2
bioconductor: MultiMed
Testing multiple biological mediators simultaneouslyPapers that mentioned: 2
bioconductor: nethet
A bioconductor package for high-dimensional exploration of biological network heterogeneityPapers that mentioned: 2
bioconductor: omicRexposome
Exposome and omic data associatin and integration analysisPapers that mentioned: 2
bioconductor: pathVar
Methods to Find Pathways with Significantly Different VariabilityPapers that mentioned: 2
bioconductor: pepXMLTab
Parsing pepXML files and filter based on peptide FDR.Papers that mentioned: 2
bioconductor: psygenet2r
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disordersPapers that mentioned: 2
bioconductor: qpcrNorm
Data-driven normalization strategies for high-throughput qPCR data.Papers that mentioned: 2
bioconductor: rain
Rhythmicity Analysis Incorporating Non-parametric MethodsPapers that mentioned: 2
bioconductor: rfPred
Assign rfPred functional prediction scores to a missense variants listPapers that mentioned: 2
bioconductor: RImmPort
RImmPort: Enabling Ready-for-analysis Immunology Research DataPapers that mentioned: 2
bioconductor: Risa
Converting experimental metadata from ISA-tab into Bioconductor data structuresPapers that mentioned: 2
bioconductor: RUVcorr
Removal of unwanted variation for gene-gene correlations and related analysisPapers that mentioned: 2
bioconductor: scBFA
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seqPapers that mentioned: 2
bioconductor: SCBN
A statistical normalization method and differential expression analysis for RNA-seq data between different speciesPapers that mentioned: 2
bioconductor: SDAMS
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing DataPapers that mentioned: 2
bioconductor: seqbias
Estimation of per-position bias in high-throughput sequencing dataPapers that mentioned: 2
bioconductor: seqsetvis
Set Based Visualizations for Next-Gen Sequencing DataPapers that mentioned: 2
bioconductor: singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq DataPapers that mentioned: 2
bioconductor: sizepower
Sample Size and Power Calculation in Micorarray StudiesPapers that mentioned: 2
bioconductor: SNPhood
SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS dataPapers that mentioned: 2
bioconductor: specL
specL - Prepare Peptide Spectrum Matches for Use in Targeted ProteomicsPapers that mentioned: 2
bioconductor: StructuralVariantAnnotation
Variant annotations for structural variantsPapers that mentioned: 2
bioconductor: TMixClust
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing SplinesPapers that mentioned: 2
bioconductor: Uniquorn
Identification of cancer cell lines based on their weighted mutational/ variational fingerprintPapers that mentioned: 2
bioconductor: Ularcirc
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)Papers that mentioned: 2
bioconductor: VegaMC
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in CancerPapers that mentioned: 2
bioconductor: XINA
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network AnalysisPapers that mentioned: 2
bioconductor: ABAEnrichment
Papers that mentioned: 2bioconductor: girafe
Genome Intervals and Read Alignments for Functional ExplorationPapers that mentioned: 1
bioconductor: MWASTools
MWASTools: an integrated pipeline to perform metabolome-wide association studiesPapers that mentioned: 1
bioconductor: GenomicDistributions
GenomicDistributions: fast analysis of genomic intervals with BioconductorPapers that mentioned: 1
bioconductor: GeneSelectMMD
Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributionsPapers that mentioned: 1
bioconductor: geneAttribution
Identification of candidate genes associated with genetic variationPapers that mentioned: 1
bioconductor: GCSscore
GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arraysPapers that mentioned: 1
bioconductor: GladiaTOX
R Package for Processing High Content Screening dataPapers that mentioned: 1
bioconductor: FunChIP
Clustering and Alignment of ChIP-Seq peaks based on their shapesPapers that mentioned: 1
bioconductor: ceRNAnetsim
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)Papers that mentioned: 1
bioconductor: FRGEpistasis
Epistasis Analysis for Quantitative Traits by Functional Regression ModelPapers that mentioned: 1
bioconductor: nnNorm
Spatial and intensity based normalization of cDNA microarray data based on robust neural netsPapers that mentioned: 1
bioconductor: npGSEA
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)Papers that mentioned: 1
bioconductor: fcScan
fcScan for detecting clusters of coordinates with user defined optionsPapers that mentioned: 1
bioconductor: fCCAC
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasetsPapers that mentioned: 1
bioconductor: FastqCleaner
A Shiny Application for Quality Control, Filtering and Trimming of FASTQ FilesPapers that mentioned: 1
bioconductor: fastLiquidAssociation
functions for genome-wide application of Liquid AssociationPapers that mentioned: 1
bioconductor: omicplotR
Visual Exploration of Omic Datasets Using a Shiny AppPapers that mentioned: 1
bioconductor: alsace
Papers that mentioned: 1bioconductor: OMICsPCA
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samplesPapers that mentioned: 1
bioconductor: epigenomix
Epigenetic and gene transcription data normalization and integration with mixture modelsPapers that mentioned: 1
bioconductor: dyebias
The GASSCO method for correcting for slide-dependent gene-specific dye biasPapers that mentioned: 1
bioconductor: DrugVsDisease
Comparison of disease and drug profiles using Gene set Enrichment AnalysisPapers that mentioned: 1
bioconductor: oneSENSE
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)Papers that mentioned: 1
bioconductor: DominoEffect
Identification and Annotation of Protein Hotspot ResiduesPapers that mentioned: 1
bioconductor: OpenStats
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype associationPapers that mentioned: 1
bioconductor: dks
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.Papers that mentioned: 1