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bioconductor projects 1,374

bioconductor: GeneAnswers
Papers that mentioned: 33
Unlikely Science (0)
bioconductor: NormqPCR
Functions for normalisation of RT-qPCR data
Papers that mentioned: 33
Very Likely Science (90)
bioconductor: TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Papers that mentioned: 33
Very Likely Science (100)
bioconductor: BiSeq
Processing and analyzing bisulfite sequencing data
Papers that mentioned: 33
Very Likely Science (100)
bioconductor: Rgraphviz
Provides plotting capabilities for R graph objects
Papers that mentioned: 33
Very Likely Science (100)
bioconductor: flowClust
Clustering for Flow Cytometry
Papers that mentioned: 33
Very Likely Science (90)
bioconductor: SomaticSignatures
Somatic Signatures
Papers that mentioned: 32
Very Likely Science (67)
bioconductor: MutationalPatterns
Comprehensive genome-wide analysis of mutational processes
Papers that mentioned: 32
Very Likely Science (100)
bioconductor: aCGH
Classes and functions for Array Comparative Genomic Hybridization data
Papers that mentioned: 32
Very Likely Science (98)
bioconductor: iClusterPlus
Integrative clustering of multi-type genomic data
Papers that mentioned: 32
Very Likely Science (65)
bioconductor: treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
Papers that mentioned: 32
Very Likely Science (100)
bioconductor: CEMiTool
Co-expression Modules identification Tool
Papers that mentioned: 31
Very Likely Science (100)
bioconductor: QDNAseq
Quantitative DNA Sequencing for Chromosomal Aberrations
Papers that mentioned: 31
Very Likely Science (100)
bioconductor: BiocParallel
Bioconductor facilities for parallel evaluation
Papers that mentioned: 30
Very Likely Science (100)
bioconductor: regioneR
Association analysis of genomic regions based on permutation tests
Papers that mentioned: 30
Very Likely Science (100)
bioconductor: affylmGUI
GUI for limma Package with Affymetrix Microarrays
Papers that mentioned: 30
Very Likely Science (78)
bioconductor: graphite
GRAPH Interaction from pathway Topological Environment
Papers that mentioned: 30
Very Likely Science (100)
bioconductor: QuasR
Quantify and Annotate Short Reads in R
Papers that mentioned: 30
Very Likely Science (90)
bioconductor: globaltest
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
Papers that mentioned: 30
Very Likely Science (90)
bioconductor: LACE
Longitudinal Analysis of Cancer Evolution (LACE)
Papers that mentioned: 29
Very Likely Science (100)
bioconductor: MIMOSA
Mixture Models for Single-Cell Assays
Papers that mentioned: 29
Very Likely Science (75)
bioconductor: csaw
ChIP-Seq Analysis with Windows
Papers that mentioned: 29
Very Likely Science (100)
bioconductor: EpiDISH
Epigenetic Dissection of Intra-Sample-Heterogeneity
Papers that mentioned: 29
Very Likely Science (100)
bioconductor: MODA
MODA: MOdule Differential Analysis for weighted gene co-expression network
Papers that mentioned: 28
Very Likely Science (100)
bioconductor: CopywriteR
Copy number information from targeted sequencing using off-target reads
Papers that mentioned: 28
Very Likely Science (100)
bioconductor: MethylAid
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Papers that mentioned: 28
Very Likely Science (100)
bioconductor: BitSeq
Papers that mentioned: 28
Unlikely Science (0)
bioconductor: oposSOM
Comprehensive analysis of transcriptome data
Papers that mentioned: 27
Very Likely Science (100)
bioconductor: systemPipeR
systemPipeR: workflow management and report generation environment
Papers that mentioned: 27
Very Likely Science (98)
bioconductor: GEOmetadb
A compilation of metadata from NCBI GEO
Papers that mentioned: 27
Very Likely Science (83)
bioconductor: PFP
Pathway Fingerprint Framework in R
Papers that mentioned: 27
Very Likely Science (83)
bioconductor: CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Papers that mentioned: 27
Very Likely Science (100)
bioconductor: HEM
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Papers that mentioned: 27
Very Likely Science (100)
bioconductor: ENmix
Quality control and analysis tools for Illumina DNA methylation BeadChip
Papers that mentioned: 27
Very Likely Science (100)
bioconductor: deepSNV
Detection of subclonal SNVs in deep sequencing data.
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: PharmacoGx
Analysis of Large-Scale Pharmacogenomic Data
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: flowViz
Visualization for flow cytometry
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: frma
Frozen RMA and Barcode
Papers that mentioned: 26
Very Likely Science (90)
bioconductor: QUBIC
An R package for qualitative biclustering in support of gene co-expression analyses
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: EBarrays
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Papers that mentioned: 26
Very Likely Science (100)
bioconductor: conumee
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Papers that mentioned: 25
Very Likely Science (100)
bioconductor: PROPER
PROspective Power Evaluation for RNAseq
Papers that mentioned: 25
Very Likely Science (98)
bioconductor: CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Papers that mentioned: 25
Very Likely Science (100)
bioconductor: cellHTS2
Analysis of cell-based screens - revised version of cellHTS
Papers that mentioned: 25
Very Likely Science (100)
bioconductor: variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments
Papers that mentioned: 25
Very Likely Science (100)
bioconductor: seqLogo
Sequence logos for DNA sequence alignments
Papers that mentioned: 24
Very Likely Science (100)
bioconductor: MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
Papers that mentioned: 24
Very Likely Science (100)
bioconductor: gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) Files
Papers that mentioned: 23
Very Likely Science (100)
bioconductor: dupRadar
Assessment of duplication rates in RNA-Seq datasets
Papers that mentioned: 23
Very Likely Science (100)
bioconductor: DeconRNASeq
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Papers that mentioned: 23
Very Likely Science (90)
bioconductor: NanoStringDiff
Differential Expression Analysis of NanoString nCounter Data
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: RTCGAToolbox
A new tool for exporting TCGA Firehose data
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: SISPA
SISPA: Method for Sample Integrated Set Profile Analysis
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: RCy3
Functions to Access and Control Cytoscape
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: RRHO
Inference on agreement between ordered lists
Papers that mentioned: 22
Very Likely Science (90)
bioconductor: EGSEA
Ensemble of Gene Set Enrichment Analyses
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: RTCGA
The Cancer Genome Atlas Data Integration
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: rbsurv
Robust likelihood-based survival modeling with microarray data
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: CancerSubtypes
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: RNASeqPower
Sample size for RNAseq studies
Papers that mentioned: 22
Very Likely Science (83)
bioconductor: HIBAG
HLA Genotype Imputation with Attribute Bagging
Papers that mentioned: 22
Very Likely Science (100)
bioconductor: DTA
Dynamic Transcriptome Analysis
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: ballgown
Flexible, isoform-level differential expression analysis
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: BASiCS
Bayesian Analysis of Single-Cell Sequencing data
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: Category
Category Analysis
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: Pi
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: CNAnorm
A normalization method for Copy Number Aberration in cancer samples
Papers that mentioned: 21
Very Likely Science (90)
bioconductor: CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: limmaGUI
GUI for limma Package With Two Color Microarrays
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: RedeR
Interactive visualization and manipulation of nested networks
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: HiTC
High Throughput Chromosome Conformation Capture analysis
Papers that mentioned: 21
Very Likely Science (75)
bioconductor: M3Drop
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: POMA
Tools for Omics Data Analysis
Papers that mentioned: 20
Very Likely Science (100)
bioconductor: MEDME
Modelling Experimental Data from MeDIP Enrichment
Papers that mentioned: 20
Very Likely Science (100)
bioconductor: IPO
Automated Optimization of XCMS Data Processing parameters
Papers that mentioned: 20
Very Likely Science (84)
bioconductor: SRAdb
A compilation of metadata from NCBI SRA and tools
Papers that mentioned: 20
Very Likely Science (100)
bioconductor: PCAtools
PCAtools: Everything Principal Components Analysis
Papers that mentioned: 20
Very Likely Science (100)
bioconductor: maanova
Tools for analyzing Micro Array experiments
Papers that mentioned: 20
Very Likely Science (100)
bioconductor: ROTS
Reproducibility-Optimized Test Statistic
Papers that mentioned: 20
Very Likely Science (90)
bioconductor: flowStats
Statistical methods for the analysis of flow cytometry data
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: mygene
Access MyGene.Info_ services
Papers that mentioned: 19
Very Likely Science (83)
bioconductor: Cardinal
A mass spectrometry imaging toolbox for statistical analysis
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: EGAD
Extending guilt by association by degree
Papers that mentioned: 19
Very Likely Science (90)
bioconductor: GeneMeta
MetaAnalysis for High Throughput Experiments
Papers that mentioned: 19
Very Likely Science (75)
bioconductor: PAA
PAA (Protein Array Analyzer)
Papers that mentioned: 19
Very Likely Science (90)
bioconductor: RPA
RPA: Robust Probabilistic Averaging for probe-level analysis
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
Papers that mentioned: 18
Very Likely Science (83)
bioconductor: HMMcopy
Copy number prediction with correction for GC and mappability bias for HTS data
Papers that mentioned: 18
Very Likely Science (90)
bioconductor: shinyMethyl
Interactive visualization for Illumina methylation arrays
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: MBASED
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: TissueEnrich
Tissue-specific gene enrichment analysis
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: coMET
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: biomformat
An interface package for the BIOM file format
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: SeqGSEA
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: Sushi
Papers that mentioned: 18
Unlikely Science (0)
bioconductor: destiny
Creates diffusion maps
Papers that mentioned: 18
Very Likely Science (100)