Data

Tools

Indexes

Applications

Experiments

Papers

bioconductor projects 1,374

bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysis
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: MEAL
Perform methylation analysis
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: omicade4
Multiple co-inertia analysis of omics datasets
Papers that mentioned: 12
Very Likely Science (85)
bioconductor: tximeta
Transcript Quantification Import with Automatic Metadata
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: AnnotationForge
Tools for building SQLite-based annotation data packages
Papers that mentioned: 11
Very Likely Science (75)
bioconductor: RiboProfiling
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Papers that mentioned: 11
Very Likely Science (75)
bioconductor: OrderedList
Similarities of Ordered Gene Lists
Papers that mentioned: 11
Very Likely Science (98)
bioconductor: openCyto
Hierarchical Gating Pipeline for flow cytometry data
Papers that mentioned: 11
Very Likely Science (75)
bioconductor: COHCAP
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: flowPeaks
An R package for flow data clustering
Papers that mentioned: 11
Very Likely Science (75)
bioconductor: TDARACNE
Papers that mentioned: 11
Unlikely Science (0)
bioconductor: compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: MetaNeighbor
Single cell replicability analysis
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: PureCN
Copy number calling and SNV classification using targeted short read sequencing
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: makecdfenv
CDF Environment Maker
Papers that mentioned: 11
Very Likely Science (83)
bioconductor: SamSPECTRAL
Identifies cell population in flow cytometry data
Papers that mentioned: 11
Very Likely Science (98)
bioconductor: Linnorm
Linear model and normality based normalization and transformation method (Linnorm)
Papers that mentioned: 11
Very Likely Science (98)
bioconductor: methylGSA
Gene Set Analysis Using the Outcome of Differential Methylation
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: Oscope
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Papers that mentioned: 11
Very Likely Science (75)
bioconductor: SPONGE
Sparse Partial Correlations On Gene Expression
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: ExperimentHub
Client to access ExperimentHub resources
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: methylSig
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Papers that mentioned: 11
Very Likely Science (100)
bioconductor: RMassBank
Workflow to process tandem MS files and build MassBank records
Papers that mentioned: 10
Very Likely Science (90)
bioconductor: ASICS
Automatic Statistical Identification in Complex Spectra
Papers that mentioned: 10
Very Likely Science (85)
bioconductor: Director
A dynamic visualization tool of multi-level data
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: Prostar
Provides a GUI for DAPAR
Papers that mentioned: 10
Very Likely Science (90)
bioconductor: miRBaseConverter
A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions
Papers that mentioned: 10
Very Likely Science (87)
bioconductor: PROPS
PRObabilistic Pathway Score (PROPS)
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: compEpiTools
Tools for computational epigenomics
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: nucleR
Nucleosome positioning package for R
Papers that mentioned: 10
Very Likely Science (90)
bioconductor: DNAshapeR
High-throughput prediction of DNA shape features
Papers that mentioned: 10
Very Likely Science (73)
bioconductor: MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
Papers that mentioned: 10
Very Likely Science (93)
bioconductor: motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Papers that mentioned: 10
Very Likely Science (98)
bioconductor: arrayQuality
Assessing array quality on spotted arrays
Papers that mentioned: 10
Very Likely Science (90)
bioconductor: Harman
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Papers that mentioned: 10
Very Likely Science (98)
bioconductor: Clomial
Infers clonal composition of a tumor
Papers that mentioned: 10
Very Likely Science (98)
bioconductor: GenomicInteractions
Utilities for handling genomic interaction data
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: RmiR
Papers that mentioned: 10
Unlikely Science (0)
bioconductor: goProfiles
goProfiles: an R package for the statistical analysis of functional profiles
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculations
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: UniProt.ws
R Interface to UniProt Web Services
Papers that mentioned: 10
Very Likely Science (100)
bioconductor: signeR
Empirical Bayesian approach to mutational signature discovery
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: SIMAT
GC-SIM-MS data processing and alaysis tool
Papers that mentioned: 9
Very Likely Science (83)
bioconductor: batchelor
Single-Cell Batch Correction Methods
Papers that mentioned: 9
Very Likely Science (90)
bioconductor: Dino
Normalization of Single-Cell mRNA Sequencing Data
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: metagene
A package to produce metagene plots
Papers that mentioned: 9
Very Likely Science (96)
bioconductor: tRNA
Analyzing tRNA sequences and structures
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: chipseq
chipseq: A package for analyzing chipseq data
Papers that mentioned: 9
Very Likely Science (90)
bioconductor: methylPipe
Base resolution DNA methylation data analysis
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: qpgraph
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: supraHex
supraHex: a supra-hexagonal map for analysing tabular omics data
Papers that mentioned: 9
Very Likely Science (98)
bioconductor: metaCCA
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: SWATH2stats
Transform and Filter SWATH Data for Statistical Packages
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: KEGGprofile
Papers that mentioned: 9
Unlikely Science (0)
bioconductor: viper
Virtual Inference of Protein-activity by Enriched Regulon analysis
Papers that mentioned: 9
Very Likely Science (100)
bioconductor: NormalyzerDE
Evaluation of normalization methods and calculation of differential expression analysis statistics
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: COSNet
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: netSmooth
Network smoothing for scRNAseq
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: clusterExperiment
Compare Clusterings for Single-Cell Sequencing
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: Metab
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
Papers that mentioned: 8
Likely Science (43)
bioconductor: sangerseqR
Tools for Sanger Sequencing Data in R
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: BatchQC
Batch Effects Quality Control Software
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: Trendy
Breakpoint analysis of time-course expression data
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: SeqArray
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: plyranges
A fluent interface for manipulating GenomicRanges
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS data
Papers that mentioned: 8
Very Likely Science (90)
bioconductor: Rdisop
Decomposition of Isotopic Patterns
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: rGADEM
de novo motif discovery
Papers that mentioned: 8
Very Likely Science (90)
bioconductor: anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: scMerge
scMerge: Merging multiple batches of scRNA-seq data
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: RCAS
RNA Centric Annotation System
Papers that mentioned: 8
Very Likely Science (90)
bioconductor: TFEA.ChIP
Analyze Transcription Factor Enrichment
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: clipper
Gene Set Analysis Exploiting Pathway Topology
Papers that mentioned: 8
Very Likely Science (85)
bioconductor: sSeq
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Papers that mentioned: 8
Very Likely Science (68)
bioconductor: CoRegNet
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: GenomicDataCommons
NIH / NCI Genomic Data Commons Access
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: HIPPO
Heterogeneity-Induced Pre-Processing tOol
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: SCAN.UPC
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: IHW
Independent Hypothesis Weighting
Papers that mentioned: 8
Very Likely Science (75)
bioconductor: Maaslin2
"Multivariable Association Discovery in Population-scale Meta-omics Studies"
Papers that mentioned: 8
Very Likely Science (90)
bioconductor: pqsfinder
Identification of potential quadruplex forming sequences
Papers that mentioned: 8
Very Likely Science (75)
bioconductor: Harshlight
A "corrective make-up" program for microarray chips
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: GRENITS
Gene Regulatory Network Inference Using Time Series
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: IMMAN
Interlog protein network reconstruction by Mapping and Mining ANalysis
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: slingshot
Tools for ordering single-cell sequencing
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: ASEB
Predict Acetylated Lysine Sites
Papers that mentioned: 8
Very Likely Science (98)
bioconductor: CSSP
ChIP-Seq Statistical Power
Papers that mentioned: 8
Very Likely Science (100)
bioconductor: FELLA
Interpretation and enrichment for metabolomics data
Papers that mentioned: 8
Very Likely Science (83)
bioconductor: riboSeqR
Analysis of sequencing data from ribosome profiling experiments
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: convert
Convert Microarray Data Objects
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: dmrseq
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: DiffLogo
DiffLogo: A comparative visualisation of biooligomer motifs
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: scds
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: S4Vectors
Foundation of vector-like and list-like containers in Bioconductor
Papers that mentioned: 7
Very Likely Science (75)
bioconductor: M3C
Monte Carlo Reference-based Consensus Clustering
Papers that mentioned: 7
Very Likely Science (90)
bioconductor: ROntoTools
R Onto-Tools suite
Papers that mentioned: 7
Very Likely Science (98)
bioconductor: AlphaBeta
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Papers that mentioned: 7
Very Likely Science (75)
bioconductor: DeMAND
DeMAND
Papers that mentioned: 7
Very Likely Science (98)