Biocview "GenomeAnnotation"

A container (S4 class) for matrix-like assays

Affinity test for identifying regularity Indels

Affinity test for identifying regulatory SNPs

Analysis of alternative splicing using RNA-Seq

Analysis of Alternative Splicing Using RNA-Seq

Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Annotation of Genomic Regions to Genomic Annotations

An R package for analysis of massive parallel sequencing based RNA structure probing data

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

A Software Suite for Shallow Sequencing Copy Number Analysis

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

A Tool for Customizable and Reproducible Plotting of Sequencing Coverage Data

A unified framework for working transparently with on-disk and in-memory array-like datasets

Client for GREAT Analysis

Collection of BioC2021 resources

Comprehensive Annotation of Predictive Features for Interval-based Genomic Data

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Conveniently access PyRanges functionalities from Bioconductor

Conveniently import and query gene models

Coordinate-Based Genomic Visualization Package for R

Coordinate Covariation Analysis

Data and functions for dealing with microRNAs

DeepBlueR

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

DNA IP-seq data analysis

dplyr-based Access to Bioconductor Annotation Resources

Efficient graph representation and manipulation in Bioconductor

Estimates Isoform Specific RPF Footprint Densities

fcScan for detecting clusters of coordinates with user defined options

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

Generate and Manipulate Genomic Ranges

Generation of null ranges via bootstrapping or covariate matching

Genometric Correlation package

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

GenomicOperations

gQTLBase: infrastructure for eQTL, mQTL and similar studies

gQTLstats: computationally efficient analysis for eQTL and allied studies

GREAT Analysis - Functional Enrichment on Genomic Regions

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

Hi-C Annotation and Graphics Ensemble

HMM-Based Model for Genotyping and Cross-Over Identification

HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models

Identification and classification of plant transcription factors

Illumina 450K methylation array spatial analysis methods

Interval-Wise Testing for Omics Data

Introduce *Ranges to bedtools users

Locus overlap analysis for enrichment of genomic ranges

Making 2D Hilbert Curve

Making Enriched Heatmaps

Manipulation of SQLite-based annotations in Bioconductor

Mapping, quantification and variant analysis of sequencing data

Mean Alterations Using Discrete Expression

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

Methylation-Based Inference of Regulatory Activity

Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Mutation on Open Reading FramE annotation

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Optimising the Definition of Expressed Regions

Optimized Functional Annotation Of ChIP-seq Data

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

Prediction of intronic splicing branchpoints

Predict MicroExons in Plant Genomes

Promoter identification from large-scale TSS profiling data

Quantitative DNA Sequencing for Chromosomal Aberrations

Query the gene models of a given organism/assembly

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Representation and manipulation of genomic intervals

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

RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

R Interface with InterMine-Powered Databases

RNA Centric Annotation System

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Significance-based Modules Integrating the Transcriptome and Epigenome

SummarizedExperiment container

The Genomic STate ANnotation Package

Tools for computational epigenomics

Tools for region- and process-centric analyses of multiple assay types

Transcript Quantification Import with Automatic Metadata

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Visualization of genomic structural variants

Biocview "GenomeAnnotation"

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