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bioconductor projects 1,374

bioconductor: NuPoP
An R package for nucleosome positioning prediction
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: biomformat
An interface package for the BIOM file format
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: destiny
Creates diffusion maps
Papers that mentioned: 18
Very Likely Science (100)
bioconductor: ALPS
Papers that mentioned: 18
Unlikely Science (0)
bioconductor: TEQC
Quality control for target capture experiments
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: TCseq
Time course sequencing data analysis
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: DRIMSeq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: Glimma
Interactive HTML graphics
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: GWASTools
Tools for Genome Wide Association Studies
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: flowMeans
Non-parametric Flow Cytometry Data Gating
Papers that mentioned: 17
Very Likely Science (90)
bioconductor: tilingArray
Transcript mapping with high-density oligonucleotide tiling arrays
Papers that mentioned: 17
Very Likely Science (90)
bioconductor: TnT
Interactive Visualization for Genomic Features
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: PECA
Probe-level Expression Change Averaging
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: MotifDb
An Annotated Collection of Protein-DNA Binding Sequence Motifs
Papers that mentioned: 17
Very Likely Science (75)
bioconductor: easyRNASeq
Count summarization and normalization for RNA-Seq data
Papers that mentioned: 17
Very Likely Science (90)
bioconductor: HELP
Tools for HELP data analysis
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: GOTHiC
Binomial test for Hi-C data analysis
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: genomation
Summary, annotation and visualization of genomic data
Papers that mentioned: 17
Very Likely Science (100)
bioconductor: genArise
Microarray Analysis tool
Papers that mentioned: 16
Very Likely Science (100)
bioconductor: edge
Extraction of Differential Gene Expression
Papers that mentioned: 16
Very Likely Science (100)
bioconductor: SPLINTER
Splice Interpreter of Transcripts
Papers that mentioned: 16
Very Likely Science (85)
bioconductor: IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Papers that mentioned: 16
Very Likely Science (90)
bioconductor: AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Papers that mentioned: 16
Very Likely Science (100)
bioconductor: PWMEnrich
PWM enrichment analysis
Papers that mentioned: 16
Very Likely Science (85)
bioconductor: scDD
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Papers that mentioned: 16
Very Likely Science (100)
bioconductor: SLqPCR
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
Papers that mentioned: 16
Very Likely Science (90)
bioconductor: snapCGH
Segmentation, normalisation and processing of aCGH data
Papers that mentioned: 16
Very Likely Science (98)
bioconductor: MAIT
Statistical Analysis of Metabolomic Data
Papers that mentioned: 16
Very Likely Science (85)
bioconductor: MultiAssayExperiment
Software for the integration of multi-omics experiments in Bioconductor
Papers that mentioned: 16
Very Likely Science (85)
bioconductor: flowDensity
Sequential Flow Cytometry Data Gating
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: DEGraph
Two-sample tests on a graph
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
Papers that mentioned: 15
Very Likely Science (75)
bioconductor: sigPathway
Pathway Analysis
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: ChIPQC
Quality metrics for ChIPseq data
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: cghMCR
Find chromosome regions showing common gains/losses
Papers that mentioned: 15
Very Likely Science (73)
bioconductor: piano
Platform for integrative analysis of omics data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: BiocGenerics
S4 generic functions used in Bioconductor
Papers that mentioned: 15
Very Likely Science (75)
bioconductor: CSAR
Statistical tools for the analysis of ChIP-seq data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: RCM
Fit row-column association models with the negative binomial distribution for the microbiome
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: DEsingle
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: PROcess
Ciphergen SELDI-TOF Processing
Papers that mentioned: 15
Very Likely Science (98)
bioconductor: PhenStat
Statistical analysis of phenotypic data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: VariantTools
Tools for Exploratory Analysis of Variant Calls
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: MetNet
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: bioDist
Different distance measures
Papers that mentioned: 15
Very Likely Science (75)
bioconductor: SCnorm
Normalization of single cell RNA-seq data
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: annotatr
Annotation of Genomic Regions to Genomic Annotations
Papers that mentioned: 15
Very Likely Science (100)
bioconductor: puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: BAC
Papers that mentioned: 14
Unlikely Science (0)
bioconductor: MEAT
Muscle Epigenetic Age Test
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: trackViewer
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: iPAC
Identification of Protein Amino acid Clustering
Papers that mentioned: 14
Very Likely Science (98)
bioconductor: CoGAPS
Coordinated Gene Activity in Pattern Sets
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: ViSEAGO
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
Papers that mentioned: 14
Very Likely Science (90)
bioconductor: Repitools
Epigenomic tools
Papers that mentioned: 14
Very Likely Science (90)
bioconductor: DropletUtils
Utilities for Handling Single-Cell Droplet Data
Papers that mentioned: 14
Very Likely Science (90)
bioconductor: cqn
Conditional quantile normalization
Papers that mentioned: 14
Very Likely Science (90)
bioconductor: SGSeq
Splice event prediction and quantification from RNA-seq data
Papers that mentioned: 14
Very Likely Science (75)
bioconductor: RBM
RBM: a R package for microarray and RNA-Seq data analysis
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
Papers that mentioned: 14
Very Likely Science (75)
bioconductor: GlobalAncova
Global test for groups of variables via model comparisons
Papers that mentioned: 14
Very Likely Science (90)
bioconductor: ATACseqQC
ATAC-seq Quality Control
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: geneplotter
Graphics related functions for Bioconductor
Papers that mentioned: 14
Very Likely Science (100)
bioconductor: singscore
Rank-based single-sample gene set scoring method
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: iSEE
Interactive SummarizedExperiment Explorer
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: RnaSeqSampleSize
RnaSeqSampleSize
Papers that mentioned: 13
Very Likely Science (90)
bioconductor: copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: miRNApath
miRNApath: Pathway Enrichment for miRNA Expression Data
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: EWCE
Expression Weighted Celltype Enrichment
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: RSVSim
RSVSim: an R/Bioconductor package for the simulation of structural variations
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: GARS
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets
Papers that mentioned: 13
Very Likely Science (85)
bioconductor: ggcyto
Visualize Cytometry data with ggplot
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: motifbreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: Rcpi
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: scde
Single Cell Differential Expression
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: Mergeomics
Integrative network analysis of omics data
Papers that mentioned: 13
Very Likely Science (85)
bioconductor: SPEM
S-system parameter estimation method
Papers that mentioned: 13
Very Likely Science (98)
bioconductor: SpidermiR
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: metaMS
MS-based metabolomics annotation pipeline
Papers that mentioned: 13
Very Likely Science (75)
bioconductor: PathNet
An R package for pathway analysis using topological information
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: Chicago
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: COCOA
Coordinate Covariation Analysis
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: affxparser
Affymetrix File Parsing SDK
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: affycomp
Graphics Toolbox for Assessment of Affymetrix Expression Measures
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: illuminaio
Parsing Illumina Microarray Output Files
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: miRNAtap
miRNAtap: microRNA Targets - Aggregated Predictions
Papers that mentioned: 12
Very Likely Science (98)
bioconductor: OLIN
Optimized local intensity-dependent normalisation of two-color microarrays
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: EnrichedHeatmap
Making Enriched Heatmaps
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: ReadqPCR
Read qPCR data
Papers that mentioned: 12
Very Likely Science (90)
bioconductor: diffHic
Differential Analyis of Hi-C Data
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: OSAT
OSAT: Optimal Sample Assignment Tool
Papers that mentioned: 12
Very Likely Science (90)
bioconductor: iCARE
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)
Papers that mentioned: 12
Very Likely Science (90)
bioconductor: HTSeqGenie
A NGS analysis pipeline.
Papers that mentioned: 12
Very Likely Science (85)
bioconductor: TIN
Transcriptome instability analysis
Papers that mentioned: 12
Very Likely Science (100)
bioconductor: categoryCompare
Meta-analysis of high-throughput experiments using feature annotations
Papers that mentioned: 12
Very Likely Science (95)