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bioconductor projects 1,374

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
Very Likely Science (100)
bioconductor: PAST
Pathway Association Study Tool (PAST)
Papers that mentioned: 2,336
Very Likely Science (100)
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
Very Likely Science (75)
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
Very Likely Science (83)
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census data
Papers that mentioned: 1,702
Very Likely Science (75)
bioconductor: affy
Methods for Affymetrix Oligonucleotide Arrays
Papers that mentioned: 989
Very Likely Science (98)
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
Very Likely Science (100)
bioconductor: MIRA
Methylation-Based Inference of Regulatory Activity
Papers that mentioned: 856
Very Likely Science (98)
bioconductor: DEGseq
Identify Differentially Expressed Genes from RNA-seq data
Papers that mentioned: 697
Very Likely Science (100)
bioconductor: MAST
Model-based Analysis of Single Cell Transcriptomics
Papers that mentioned: 668
Very Likely Science (100)
bioconductor: topGO
Enrichment Analysis for Gene Ontology
Papers that mentioned: 652
Very Likely Science (100)
bioconductor: COMPASS
Combinatorial Polyfunctionality Analysis of Single Cells
Papers that mentioned: 614
Very Likely Science (100)
bioconductor: ComplexHeatmap
Make Complex Heatmaps
Papers that mentioned: 565
Very Likely Science (90)
bioconductor: SIM
Integrated Analysis on two human genomic datasets
Papers that mentioned: 554
Very Likely Science (100)
bioconductor: RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA)
Papers that mentioned: 516
Very Likely Science (90)
bioconductor: sva
Surrogate Variable Analysis
Papers that mentioned: 511
Very Likely Science (100)
bioconductor: minfi
Analyze Illumina Infinium DNA methylation arrays
Papers that mentioned: 506
Very Likely Science (100)
bioconductor: ADAM
ADAM: Activity and Diversity Analysis Module
Papers that mentioned: 482
Very Likely Science (100)
bioconductor: ACE
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Papers that mentioned: 478
Very Likely Science (100)
bioconductor: ggtree
an R package for visualization of tree and annotation data
Papers that mentioned: 474
Very Likely Science (100)
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
Very Likely Science (100)
bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
Very Likely Science (75)
bioconductor: DECIPHER
Tools for curating, analyzing, and manipulating biological sequences
Papers that mentioned: 415
Very Likely Science (98)
bioconductor: mixOmics
Omics Data Integration Project
Papers that mentioned: 375
Very Likely Science (90)
bioconductor: GOstats
Tools for manipulating GO and microarrays
Papers that mentioned: 368
Very Likely Science (100)
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
Very Likely Science (100)
bioconductor: CMA
Synthesis of microarray-based classification
Papers that mentioned: 337
Very Likely Science (93)
bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing data
Papers that mentioned: 331
Very Likely Science (100)
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
Very Likely Science (100)
bioconductor: GenomicRanges
Representation and manipulation of genomic intervals
Papers that mentioned: 323
Very Likely Science (90)
bioconductor: NOISeq
Exploratory analysis and differential expression for RNA-seq data
Papers that mentioned: 321
Very Likely Science (100)
bioconductor: GEM
GEM: fast association study for the interplay of Gene, Environment and Methylation
Papers that mentioned: 317
Very Likely Science (73)
bioconductor: ConsensusClusterPlus
ConsensusClusterPlus
Papers that mentioned: 313
Likely Science (50)
bioconductor: DSS
Dispersion shrinkage for sequencing data
Papers that mentioned: 288
Very Likely Science (91)
bioconductor: maftools
Summarize, Analyze and Visualize MAF Files
Papers that mentioned: 288
Very Likely Science (100)
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Papers that mentioned: 276
Very Likely Science (100)
bioconductor: dada2
Accurate, high-resolution sample inference from amplicon sequencing data
Papers that mentioned: 274
Very Likely Science (100)
bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq data
Papers that mentioned: 261
Very Likely Science (100)
bioconductor: GPA
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
Papers that mentioned: 260
Very Likely Science (100)
bioconductor: CAFE
Chromosmal Aberrations Finder in Expression data
Papers that mentioned: 251
Very Likely Science (75)
bioconductor: enrichplot
Visualization of Functional Enrichment Result
Papers that mentioned: 249
Very Likely Science (100)
bioconductor: qvalue
Q-value estimation for false discovery rate control
Papers that mentioned: 248
Very Likely Science (100)
bioconductor: GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Papers that mentioned: 243
Very Likely Science (100)
bioconductor: lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Papers that mentioned: 238
Very Likely Science (100)
bioconductor: DEXSeq
Inference of differential exon usage in RNA-Seq
Papers that mentioned: 226
Very Likely Science (100)
bioconductor: Biostrings
Efficient manipulation of biological strings
Papers that mentioned: 220
Very Likely Science (65)
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
Very Likely Science (100)
bioconductor: RankProd
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Papers that mentioned: 213
Very Likely Science (100)
bioconductor: ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Papers that mentioned: 208
Very Likely Science (100)
bioconductor: SNPRelate
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Papers that mentioned: 204
Very Likely Science (100)
bioconductor: oligo
Preprocessing tools for oligonucleotide arrays
Papers that mentioned: 204
Very Likely Science (90)
bioconductor: arrayQualityMetrics
Quality metrics report for microarray data sets
Papers that mentioned: 190
Very Likely Science (100)
bioconductor: gcrma
Background Adjustment Using Sequence Information
Papers that mentioned: 186
Very Likely Science (73)
bioconductor: DART
Denoising Algorithm based on Relevance network Topology
Papers that mentioned: 182
Very Likely Science (100)
bioconductor: FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data
Papers that mentioned: 177
Very Likely Science (75)
bioconductor: TOAST
Tools for the analysis of heterogeneous tissues
Papers that mentioned: 174
Very Likely Science (100)
bioconductor: GENIE3
GEne Network Inference with Ensemble of trees
Papers that mentioned: 172
Very Likely Science (100)
bioconductor: ReactomePA
Reactome Pathway Analysis
Papers that mentioned: 171
Very Likely Science (100)
bioconductor: metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
Papers that mentioned: 169
Very Likely Science (100)
bioconductor: muscle
Multiple Sequence Alignment with MUSCLE
Papers that mentioned: 166
Very Likely Science (100)
bioconductor: affyPLM
Methods for fitting probe-level models
Papers that mentioned: 162
Very Likely Science (100)
bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Papers that mentioned: 161
Very Likely Science (100)
bioconductor: Mfuzz
Soft clustering of time series gene expression data
Papers that mentioned: 160
Very Likely Science (100)
bioconductor: multtest
Resampling-based multiple hypothesis testing
Papers that mentioned: 158
Very Likely Science (98)
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Papers that mentioned: 155
Very Likely Science (100)
bioconductor: DNAcopy
DNA Copy Number Data Analysis
Papers that mentioned: 154
Very Likely Science (100)
bioconductor: methylKit
DNA methylation analysis from high-throughput bisulfite sequencing results
Papers that mentioned: 154
Very Likely Science (75)
bioconductor: fgsea
Fast Gene Set Enrichment Analysis
Papers that mentioned: 150
Very Likely Science (100)
bioconductor: STAN
The Genomic STate ANnotation Package
Papers that mentioned: 150
Very Likely Science (90)
bioconductor: preprocessCore
A collection of pre-processing functions
Papers that mentioned: 146
Very Likely Science (100)
bioconductor: RnBeads
RnBeads
Papers that mentioned: 145
Very Likely Science (90)
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Papers that mentioned: 145
Very Likely Science (76)
bioconductor: pathview
a tool set for pathway based data integration and visualization
Papers that mentioned: 144
Very Likely Science (100)
bioconductor: genefilter
genefilter: methods for filtering genes from high-throughput experiments
Papers that mentioned: 142
Very Likely Science (75)
bioconductor: GenomicFeatures
Conveniently import and query gene models
Papers that mentioned: 141
Very Likely Science (90)
bioconductor: baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
Papers that mentioned: 139
Very Likely Science (100)
bioconductor: LEA
LEA: an R package for Landscape and Ecological Association Studies
Papers that mentioned: 139
Very Likely Science (100)
bioconductor: Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Papers that mentioned: 138
Very Likely Science (90)
bioconductor: DOSE
Disease Ontology Semantic and Enrichment analysis
Papers that mentioned: 138
Very Likely Science (100)
bioconductor: ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Papers that mentioned: 136
Very Likely Science (100)
bioconductor: GenomicAlignments
Representation and manipulation of short genomic alignments
Papers that mentioned: 134
Very Likely Science (90)
bioconductor: Gviz
Plotting data and annotation information along genomic coordinates
Papers that mentioned: 134
Very Likely Science (100)
bioconductor: goseq
Gene Ontology analyser for RNA-seq and other length biased data
Papers that mentioned: 132
Very Likely Science (100)
bioconductor: DMRcate
Methylation array and sequencing spatial analysis methods
Papers that mentioned: 132
Very Likely Science (100)
bioconductor: NeighborNet
Neighbor_net analysis
Papers that mentioned: 131
Very Likely Science (100)
bioconductor: pcaMethods
A collection of PCA methods
Papers that mentioned: 129
Very Likely Science (100)
bioconductor: MOMA
Multi Omic Master Regulator Analysis
Papers that mentioned: 128
Very Likely Science (100)
bioconductor: EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
Papers that mentioned: 123
Very Likely Science (100)
bioconductor: ROC
utilities for ROC, with microarray focus
Papers that mentioned: 123
Very Likely Science (100)
bioconductor: ShortRead
FASTQ input and manipulation
Papers that mentioned: 119
Very Likely Science (90)
bioconductor: maSigPro
Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Papers that mentioned: 119
Very Likely Science (100)
bioconductor: GOSemSim
GO-terms Semantic Similarity Measures
Papers that mentioned: 118
Very Likely Science (90)
bioconductor: survcomp
Performance Assessment and Comparison for Survival Analysis
Papers that mentioned: 117
Very Likely Science (100)
bioconductor: MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Papers that mentioned: 115
Very Likely Science (100)
bioconductor: microbiome
Microbiome Analytics
Papers that mentioned: 114
Very Likely Science (100)
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
Very Likely Science (100)
bioconductor: PROMISE
PRojection Onto the Most Interesting Statistical Evidence
Papers that mentioned: 111
Very Likely Science (100)
bioconductor: flowCore
flowCore: Basic structures for flow cytometry data
Papers that mentioned: 109
Very Likely Science (75)