Biocview "Annotation"

Accesses MyVariant.info variant query and annotation services

Access MyGene.Info_ services

A client for retrieving Bioconductor objects from AnnotationHub

A container (S4 class) for matrix-like assays

Affymetrix Quality Assessment and Analysis Tool

alternative CDF environments (aka probeset mappings)

Analysis and Visualisation of the Human Phenotype Ontology

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of single-cell epigenomics datasets with a Shiny App

Analysis Tools for 10X V(D)J Data

Analytical R tools for Mass Spectrometry

An interface to the Semantic MEDLINE database

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

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 of Genetic Variants

Annotation of Genomic Regions to Genomic Annotations

Annotation tools for Affymetrix biological metadata

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 To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

A Software Suite for Shallow Sequencing Copy Number Analysis

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

Assign rfPred functional prediction scores to a missense variants list

A Tool for Customizable and Reproducible Plotting of Sequencing Coverage 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 universal enrichment tool for interpreting omics data

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

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 that result in large number of genomic interval data

BioThings Client (https://github.com/biothings/BioThingsClient.R)

Broadcast data between R and Gaggle

Build Annotation From Online Database

Calculate, visualize and analyse overlap between genomic regions

Category Analysis

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

ChIP-Seq Analysis with Windows

circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Classifier for Single-cell RNA-seq Using Cell Clusters

Client-side REST access KEGG

Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

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

Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Conveniently access PyRanges functionalities from Bioconductor

Conveniently import and query gene models

Convenient R wrapper of popular RNAseq pipelines designed to simplify data analysis

Converting experimental metadata from ISA-tab into Bioconductor data structures

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Creating and Using (Chemical) Compound Annotation Databases

Cross Platform Meta-Analysis of Microarray Data

Cut rDNA Sequences Into Domains Using Covariance Models

Data-driven Annotation of the Transcriptome

Data Package for the annoFuse Bioconductor Package

DBI to construct MeSH-related package from sqlite file

DeepBlueR

Delayed?Array with remote, e.g., HDF5Server or BigQuery, back end

Delineate outstanding genomic zones of differential gene activity

de novo Annotation of Pack-TYPE Transposable Elements

Detect Programmed Ribosomal Frameshifting Events from mRNA/cDNA BLASTX Output

dgeAnalysis

Differential Coverage package

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

Easy single cell analysis platform for enrichment

Efficient graph representation and manipulation in Bioconductor

Efficient, Scalable, and Reproducible Enrichment Workflows

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

epigenomic road map adventures

Exploration and Significant Biology on a Gene Set.

Exploration of marker-gene sequence taxonomic annotations

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

Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Filtering of coding and non-coding genetic variants

find influential TF and Target based on multi-omics data

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

Fix gene symbols that are messed up by Excel

flexible pipelines for secretome prediction

Functional Enrichment analysis

Functional Gene Networks derived from biological enrichment analyses

Functionality Visualization for Motifs

Functions for annotating GRanges objects

Functions for Multinomial Occupancy Distribution

Functions used to preprocess datasets stored in BioDataome

geneChip Analysis Package

Generation of null ranges via bootstrapping or covariate matching

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

Genometric Correlation package

Global visualization tool of genomic data

goProfiles: an R package for the statistical analysis of functional profiles

GO-terms Semantic Similarity Measures

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

High-quality circular visualization of omics data

High-resolution exploration of SRA metadata and RNA-seq in AnVIL

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

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 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

Information Accretion-based Function Predictor Evaluation

Infrastructure for Biostrings-based genome data packages

Infrastructure to work with genomewide position-specific scores

Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

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 Call Programs from Infernal RNA Covariance Model Package

Introduce *Ranges to bedtools users

Iterative Binary Biclustering of Genesets

Labels normalized cells for CyTOF data and assigns probabilities for each label

Manipulation of SQLite-based annotations in Bioconductor

Mean Alterations Using Discrete Expression

MeSH Enrichment and Semantic analyses

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

Methods for TCR single-cell embedding

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.

OmniPath web service client and more

OnASSIs Ontology Annotation and Semantic SImilarity software

Optimized Functional Annotation Of ChIP-seq Data

Perform Needleman-Wunsch algorithm

Phenotype Consensus ANalysis (PCAN)

Platform Design Information Package Builder

Plot Gene Ontology and KEGG pathway Annotation and Abundance

Plot Multiple Sequence Alignment using 'ggplot2'

Position-Dependent Kernel Association Test

Preprocessing of spectra data from high resolution mass spectrometry

Protein annotation data package builder

Protein Profiling

Quantification of the Tumor Immune contexture from RNA-seq data

Querying annotation data from the high performance Cellbase web

Query the gene models of a given organism/assembly

RBioinf

Reactome Pathway Analysis

Reduce + Visualize GO

Reference-Based Single-Cell RNA-Seq Annotation

Representation and manipulation of genomic intervals

Representation and manipulation of genomic intervals; demo with github actions binary generation

Retrieval from the ENVISION bioinformatics data portal into R

Retrotransposed transcript detection from structural variants

Retroviral Integration Pattern Analysis Tool (RIPAT)

R Interface to Ensembl Variant Effect Predictor

R interface to genome annotation files and the UCSC genome browser

R Interface to UniProt Web Services

rnaSeq secondary analyses

R Wrapper for DGIdb

R wrapper for the OMA REST API

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)

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 to enable the smooth interfacing of different database packages

Standard Input and Output for Bioconductor Packages

statistical analysis and visualization of functional profiles for genes and gene clusters

Statistical analysis of high-throughput RNAi screens

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

SummarizedExperiment container

Summary, annotation and visualization of genomic data

Support package for GenomicFeatures

The BRENDA Enzyme Database

The package can implement the network-based metabolite pathway identification of pathways.

Tools for Assessing Clustering

Tools for building SNPlocs 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 the FOBI Ontology

Tools for working with diverse immune genes

Transcriptome CUTteR

Transcript Quantification Import with Automatic Metadata

Transform and Filter SWATH Data for Statistical Packages

TSS sequencing data analysis

Untargeted LC-MS data annotation

Using biobtree tool from R

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.

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

Visualization of Functional Enrichment Result

Weighting protein-protein interactions

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

Yet Another Gene Ontology Package

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Biocview "Annotation"

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