Biocview "Annotation"

Accesses MyVariant.info variant query and annotation services
Accesses MyVariant.info variant query and annotation services
Access MyGene.Info_ services
Access MyGene.Info_ services
Access MyGene.Info_ services
A client for retrieving Bioconductor objects from AnnotationHub
Affymetrix Quality Assessment and Analysis Tool
alternative CDF environments (aka probeset mappings)
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Annotate sequences with KEGG pathways
Annotate transcripts and predicted protein sequences
Annotation, analysis and visualization of circRNA data
Annotation for microarrays
Annotation for microarrays
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genomic Regions to Genomic Annotations
Annotation of Genomic Regions to Genomic Annotations
Annotation tools for Affymetrix biological metadata
An R interface to the Ontology Lookup Service
An R interface to the Ontology Lookup Service
An R Package For Geneset Enrichment Workflows
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
A set of annotation maps describing the entire PANTHER Gene Ontology
A Software Suite for Shallow Sequencing Copy Number Analysis
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
Assign rfPred functional prediction scores to a missense variants list
A toolkit for APA analysis using RNA-seq data
A toolkit for APA analysis using RNA-seq data
A toolkit for single-cell immune receptor profiling
A unified framework for working transparently with on-disk and in-memory array-like datasets
A unified framework for working transparently with on-disk and in-memory array-like datasets
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
BioThings Client (https://github.com/biothings/BioThingsClient.R)
BioThings Client (https://github.com/biothings/BioThingsClient.R)
Broadcast data between R and Gaggle
Build Annotation From Online Database
Category Analysis
Category Analysis
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Client-side REST access KEGG
Client-side REST access to KEGG
Client-side REST access to KEGG
Code for using BridgeDb identifier mapping framework from within R
Code for using BridgeDb identifier mapping framework from within R
Code to convert quantities, using the QUDT ontology
Collate Gene Annotation Data from Uniprot and NIH Gene Databases
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Conveniently access PyRanges functionalities from Bioconductor
Conveniently import and query gene models
Conveniently import and query gene models
Convenient R wrapper of popular RNAseq pipelines designed to simplify data analysis
Convenient R wrapper of popular RNAseq pipelines designed to simplify data analysis
Converting experimental metadata from ISA-tab into Bioconductor data structures
Converting experimental metadata from ISA-tab into Bioconductor data structures
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cut rDNA Sequences Into Domains Using Covariance Models
DBI to construct MeSH-related package from sqlite file
DeepBlueR
DeepBlueR
DeepBlueR
Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end
Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
de novo Annotation of Pack-TYPE Transposable Elements
de novo Annotation of Pack-TYPE Transposable Elements
dgeAnalysis
Differential Coverage package
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Distributed Annotation System in R
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
dplyr-based Access to Bioconductor Annotation Resources
dplyr-based Access to Bioconductor Annotation Resources
Easy single cell analysis platform for enrichment
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Efficient graph representation and manipulation in Bioconductor
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
epigenomic road map adventures
Exploration and Significant Biology on a Gene Set.
Exploration of marker-gene sequence taxonomic annotations
Exploration of marker-gene sequence taxonomic annotations
explore metrics for sample annotation for genomic experiments
explore metrics for sample annotation for genomic experiments
Export plotting files to the xmapBridge for visualisation in X:Map
External data sets for clustifyr
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Facilities for Filtering Bioconductor Annotation Resources
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Filtering of coding and non-coding genetic variants
Filtering of coding and non-coding genetic variants
Finding the DNA and protein sequences in a list of genomic or proteomic loci
Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
flexible pipelines for secretome prediction
Functional Enrichment analysis
Functional Enrichment analysis
Functional Gene Networks derived from biological enrichment analyses
Functionality Visualization for Motifs
Functions for annotating GRanges objects
Functions for annotating GRanges objects
Functions for Multinomial Occupancy Distribution
Functions used to preprocess datasets stored in BioDataome
geneChip Analysis Package
Geneset enrichment based on InterPro domain signatures
Gene transfer format files for common ChIP-seq model organisms
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Genome sequencing project metadata
Genome sequencing project metadata
Genometric Correlation package
Global visualization tool of genomic data
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
High-quality circular visualization of omics data
HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models.
Human ChIP-seq peaks data from ENCODE and ROADMAP Epigenomics
Hyper Enrichment
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify Metabolic Subpathways Mediated by MicroRNAs
Identify Moonlighting ncRNAs
ID Mapping Analysis
ID Mapping Data Retrieval
ID Mapping Data Retrieval
Information Accretion-based Function Predictor Evaluation
Infrastructure for Biostrings-based genome data packages
Infrastructure to work with genomewide position-specific scores
Infrastructure to work with genomewide position-specific scores
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Integrative analysis of structural variations
Integrative analysis of structural variations
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interface to BioMart databases (i.e. Ensembl)
Interface to BioMart databases (i.e. Ensembl)
Interface to Call Programs from Infernal RNA Covariance Model Package
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Iterative Binary Biclustering of Genesets
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-data and tools for E. coli
miRNApath: Pathway Enrichment for miRNA Expression Data
mirtarbase: a database of validated miRNA target gene interactions
Motifs in Tandem with One Another
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Phenotype Consensus ANalysis (PCAN)
Platform Design Information Package Builder
Platform Design Information Package Builder
Platform Design Information Package Builder
Platform Design Information Package Builder
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Position-Dependent Kernel Association Test
Position-Dependent Kernel Association Test
Preprocessing of spectra data from high resolution mass spectrometry
Protein annotation data package builder
Protein Profiling
Querying annotation data from the high performance Cellbase web
Querying annotation data from the high performance Cellbase web
RBioinf
Reactome Pathway Analysis
Reactome Pathway Analysis
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference Index for Cell Types
Representation and manipulation of genomic intervals
Representation and manipulation of genomic intervals
Retrieval from the ENVISION bioinformatics data portal into R
Retroviral Integration Pattern Analysis Tool
R Interface to Ensembl Variant Effect Predictor
R Interface to Ensembl Variant Effect Predictor
R interface to genome annotation files and the UCSC genome browser
R Interface to UniProt Web Services
R Interface to UniProt Web Services
rnaSeq secondary analyses
R Wrapper for DGIdb
R Wrapper for DGIdb
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the OMA REST API
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
Select gold standard including positive and negative genes pairs based on the Gene Ontology
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Simple and fast batch gene id conversion.
Simple and fast batch gene id conversion.
Single-Cell Operation for Neat Enrichment
Software infrastructure for efficient representation of full genomes and their SNPs
Software infrastructure for efficient representation of full genomes and their SNPs
Software to enable the smooth interfacing of different database packages
Software to enable the smooth interfacing of different database packages
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical analysis of high-throughput RNAi screens
SummarizedExperiment container
SummarizedExperiment container
SummarizedExperiment container
Summary, annotation and visualization of genomic data
Summary, annotation and visualization of genomic data
Support package for GenomicFeatures
The BRENDA Enzyme Database
The BRENDA Enzyme Database
The package can implement the network-based metabolite pathway identification of pathways.
Tools for building SQLite-based annotation data packages
Tools for building SQLite-based annotation data packages
Tools for conducting enrichment analysis of MeSH
Tools for Connectivity Map-like analyses
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Transform and Filter SWATH Data for Statistical Packages
Transform and Filter SWATH Data for Statistical Packages
Using biobtree tool from R
Using biobtree tool from R
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Variant annotations for structural variants
Variant annotations for structural variants
Variant annotations for structural variants
Very simple high level analysis of Affymetrix data
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
What the package does (short line)
What the Package Does TODOELI
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Yet Another Gene Ontology Package