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: categoryCompare
Meta-analysis of high-throughput experiments using feature annotationsPapers that mentioned: 12
bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)Papers that mentioned: 12
bioconductor: methylGSA
Gene Set Analysis Using the Outcome of Differential MethylationPapers that mentioned: 11
bioconductor: SamSPECTRAL
Identifies cell population in flow cytometry dataPapers that mentioned: 11
bioconductor: methylSig
MethylSig: Differential Methylation Testing for WGBS and RRBS DataPapers that mentioned: 11
bioconductor: PureCN
Copy number calling and SNV classification using targeted short read sequencingPapers that mentioned: 11
bioconductor: openCyto
Hierarchical Gating Pipeline for flow cytometry dataPapers that mentioned: 11
bioconductor: Linnorm
Linear model and normality based normalization and transformation method (Linnorm)Papers that mentioned: 11
bioconductor: Oscope
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seqPapers that mentioned: 11
bioconductor: RiboProfiling
Ribosome Profiling Data Analysis: from BAM to Data Representation and InterpretationPapers that mentioned: 11
bioconductor: AnnotationForge
Tools for building SQLite-based annotation data packagesPapers that mentioned: 11
bioconductor: COHCAP
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq DataPapers that mentioned: 11
bioconductor: tximeta
Transcript Quantification Import with Automatic MetadataPapers that mentioned: 11
bioconductor: TDARACNE
Papers that mentioned: 11bioconductor: compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methodsPapers that mentioned: 11
bioconductor: MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containersPapers that mentioned: 10
bioconductor: Harman
The removal of batch effects from datasets using a PCA and constrained optimisation based techniquePapers that mentioned: 10
bioconductor: BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculationsPapers that mentioned: 10
bioconductor: RmiR
Papers that mentioned: 10bioconductor: ASICS
Automatic Statistical Identification in Complex SpectraPapers that mentioned: 10
bioconductor: RMassBank
Workflow to process tandem MS files and build MassBank recordsPapers that mentioned: 10
bioconductor: goProfiles
goProfiles: an R package for the statistical analysis of functional profilesPapers that mentioned: 10
bioconductor: miRBaseConverter
A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versionsPapers that mentioned: 10
bioconductor: GenomicInteractions
Utilities for handling genomic interaction dataPapers that mentioned: 10
bioconductor: motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequencePapers that mentioned: 10
bioconductor: SWATH2stats
Transform and Filter SWATH Data for Statistical PackagesPapers that mentioned: 9
bioconductor: signeR
Empirical Bayesian approach to mutational signature discoveryPapers that mentioned: 9
bioconductor: viper
Virtual Inference of Protein-activity by Enriched Regulon analysisPapers that mentioned: 9
bioconductor: DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataPapers that mentioned: 9
bioconductor: metaCCA
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation AnalysisPapers that mentioned: 9
bioconductor: qpgraph
Estimation of genetic and molecular regulatory networks from high-throughput genomics dataPapers that mentioned: 9
bioconductor: supraHex
supraHex: a supra-hexagonal map for analysing tabular omics dataPapers that mentioned: 9
bioconductor: KEGGprofile
Papers that mentioned: 9bioconductor: Harshlight
A "corrective make-up" program for microarray chipsPapers that mentioned: 8
bioconductor: SeqArray
Data Management of Large-Scale Whole-Genome Sequence Variant CallsPapers that mentioned: 8
bioconductor: pqsfinder
Identification of potential quadruplex forming sequencesPapers that mentioned: 8
bioconductor: Metab
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.Papers that mentioned: 8
bioconductor: SCAN.UPC
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)Papers that mentioned: 8
bioconductor: Maaslin2
"Multivariable Association Discovery in Population-scale Meta-omics Studies"Papers that mentioned: 8
bioconductor: anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seqPapers that mentioned: 8
bioconductor: CoRegNet
CoRegNet : reconstruction and integrated analysis of co-regulatory networksPapers that mentioned: 8
bioconductor: sSeq
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample sizePapers that mentioned: 8
bioconductor: clusterExperiment
Compare Clusterings for Single-Cell SequencingPapers that mentioned: 8
bioconductor: IMMAN
Interlog protein network reconstruction by Mapping and Mining ANalysisPapers that mentioned: 8
bioconductor: cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS dataPapers that mentioned: 8
bioconductor: NormalyzerDE
Evaluation of normalization methods and calculation of differential expression analysis statisticsPapers that mentioned: 8
bioconductor: COSNet
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelingsPapers that mentioned: 8
bioconductor: ExpressionAtlas
Download datasets from EMBL-EBI Expression AtlasPapers that mentioned: 7
bioconductor: CGHnormaliter
Normalization of array CGH data with imbalanced aberrations.Papers that mentioned: 7
bioconductor: exomeCopy
Copy number variant detection from exome sequencing read depthPapers that mentioned: 7
bioconductor: hopach
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)Papers that mentioned: 7
bioconductor: FGNet
Functional Gene Networks derived from biological enrichment analysesPapers that mentioned: 7
bioconductor: gemini
GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screensPapers that mentioned: 7
bioconductor: SMITE
Significance-based Modules Integrating the Transcriptome and EpigenomePapers that mentioned: 7
bioconductor: STATegRa
Classes and methods for multi-omics data integrationPapers that mentioned: 7
bioconductor: BioQC
Detect tissue heterogeneity in expression profiles with gene setsPapers that mentioned: 7