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: Rcade
Papers that mentioned: 1bioconductor: R3CPET
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet ProcessPapers that mentioned: 1
bioconductor: bnbc
Bandwise normalization and batch correction of Hi-C dataPapers that mentioned: 1
bioconductor: rama
Papers that mentioned: 1bioconductor: RaggedExperiment
Representation of Sparse Experiments and Assays Across SamplesPapers that mentioned: 1
bioconductor: R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer SystemPapers that mentioned: 1
bioconductor: RNAinteract
Estimate Pairwise Interactions from multidimensional featuresPapers that mentioned: 1
bioconductor: proDA
Differential Abundance Analysis of Label-Free Mass Spectrometry DataPapers that mentioned: 1
bioconductor: proBatch
Tools for Diagnostics and Corrections of Batch Effects in ProteomicsPapers that mentioned: 1
bioconductor: ppiStats
Papers that mentioned: 1bioconductor: predictionet
Papers that mentioned: 1bioconductor: perturbatr
Papers that mentioned: 1bioconductor: periodicDNA
Set of tools to identify periodic occurrences of k-mers in DNA sequencesPapers that mentioned: 1
bioconductor: PoTRA
Papers that mentioned: 1bioconductor: psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and VisualisationPapers that mentioned: 1
bioconductor: plotGrouper
Shiny app GUI wrapper for ggplot with built-in statistical analysisPapers that mentioned: 1
bioconductor: KBoost
Inference of gene regulatory networks from gene expression dataPapers that mentioned: 1
bioconductor: LineagePulse
Differential expression analysis and model fitting for single-cell RNA-seq dataPapers that mentioned: 1
bioconductor: RTNsurvival
Survival analysis using transcriptional networks inferred by the RTN packagePapers that mentioned: 1
bioconductor: RTopper
This package is designed to perform Gene Set Analysis across multiple genomic platformsPapers that mentioned: 1
bioconductor: lionessR
Modeling networks for individual samples using LIONESSPapers that mentioned: 1
bioconductor: TTMap
Two-Tier Mapper: a clustering tool based on topological data analysisPapers that mentioned: 1
bioconductor: gwasurvivr
gwasurvivr: an R package for genome wide survival analysisPapers that mentioned: 1
bioconductor: ImmuneSpaceR
A Thin Wrapper around the ImmuneSpace Data and Tools PortalPapers that mentioned: 1
bioconductor: sagenhaft
Collection of functions for reading and comparing SAGE librariesPapers that mentioned: 1
bioconductor: ILoReg
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq dataPapers that mentioned: 1
bioconductor: HPAanalyze
Retrieve and analyze data from the Human Protein AtlasPapers that mentioned: 1
bioconductor: HDTD
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)Papers that mentioned: 1
bioconductor: HPAStainR
Queries the Human Protein Atlas Staining Data for Multiple Proteins and GenesPapers that mentioned: 1
bioconductor: glmSparseNet
Network Centrality Metrics for Elastic-Net Regularized ModelsPapers that mentioned: 1
bioconductor: Sconify
A toolkit for performing KNN-based statistics for flow and mass cytometry dataPapers that mentioned: 1
bioconductor: genphen
Papers that mentioned: 1bioconductor: GNET2
Constructing gene regulatory networks from expression data through functional module inferencePapers that mentioned: 1
bioconductor: scRecover
scRecover for imputation of single-cell RNA-seq dataPapers that mentioned: 1
bioconductor: gpart
Papers that mentioned: 1bioconductor: scTensor
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decompositionPapers that mentioned: 1
bioconductor: cBioPortalData
Exposes and makes available data from the cBioPortal web resourcesPapers that mentioned: 1
bioconductor: GeneTonic
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment AnalysisPapers that mentioned: 1
bioconductor: seq2pathway
a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing dataPapers that mentioned: 1
bioconductor: seqCNA
Copy number analysis of high-throughput sequencing cancer dataPapers that mentioned: 1
bioconductor: seqPattern
Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequencesPapers that mentioned: 1
bioconductor: BiocStyle
Standard styles for vignettes and other Bioconductor documentsPapers that mentioned: 1
bioconductor: multiHiCcompare
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are availablePapers that mentioned: 1
bioconductor: multiGSEA
Combining GSEA-based pathway enrichment with multi omics data integrationPapers that mentioned: 1
bioconductor: Onassis
Papers that mentioned: 1bioconductor: SigCheck
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadataPapers that mentioned: 1
bioconductor: flowcatchR
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cellsPapers that mentioned: 1
bioconductor: GAPGOM
GAPGOM (novel Gene Annotation Prediction and other GO Metrics)Papers that mentioned: 1
bioconductor: fishpond
Fishpond: downstream methods and tools for expression dataPapers that mentioned: 1
bioconductor: gaia
Papers that mentioned: 1bioconductor: fmrs
Variable Selection in Finite Mixture of AFT Regression and FMR ModelsPapers that mentioned: 1
bioconductor: GeneAccord
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patientsPapers that mentioned: 1
bioconductor: sincell
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq dataPapers that mentioned: 1
bioconductor: exomePeak2
Peak Calling and differential analysis for MeRIP-SeqPapers that mentioned: 1
bioconductor: xmapbridge
Export plotting files to the xmapBridge for visualisation in X:MapPapers that mentioned: 1
bioconductor: slalom
Factorial Latent Variable Modeling of Single-Cell RNA-Seq DataPapers that mentioned: 1
bioconductor: epihet
Determining Epigenetic Heterogeneity from Bisulfite Sequencing DataPapers that mentioned: 1
bioconductor: SNAGEE
Signal-to-Noise applied to Gene Expression ExperimentsPapers that mentioned: 1
bioconductor: diffUTR
diffUTR: Streamlining differential exon and 3' UTR usagePapers that mentioned: 1
bioconductor: bioassayR
Cross-target analysis of small molecule bioactivityPapers that mentioned: 1
bioconductor: soGGi
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic IntervalsPapers that mentioned: 1
bioconductor: diffloop
Papers that mentioned: 1bioconductor: easyreporting
Helps creating report for improving Reproducible Computational ResearchPapers that mentioned: 1
bioconductor: BiocPkgTools
Collection of simple tools for learning about Bioconductor PackagesPapers that mentioned: 1
bioconductor: dualKS
Papers that mentioned: 1bioconductor: EmpiricalBrownsMethod
Uses Brown's method to combine p-values from dependent testsPapers that mentioned: 1