Biocview "FunctionalGenomics"

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Analysis of Transposable Elements

Analyze massively parallel reporter assays

Annotation of Genomic Regions to Genomic Annotations

An R interface to the Rfam database

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

An R package to detect chromatin state switches from epigenomic data

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

An R toolkit for non-coding RNA

askoR - Differential Expresion Analysis using edgeR

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

Automated genomic fine-mapping

Basic peak calling on STARR-seq data

Binding site defintion based on iCLIP data

Building Expression Atlas from RNA-Seq data

Candidate Gene Miner

Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information

Collection of BioC2021 resources

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

Companion package to chipenrich

Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Comparison, Benchmarking & QC of Epigenomic Datasets

Comprehensive Annotation of Predictive Features for Interval-based Genomic Data

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

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Compute the automorphisms between DNA's Abelian group representations

Coordinate-Based Genomic Visualization Package for R

Coordinate Covariation Analysis

decoupleR: Ensemble of computational methods to infer biological activities from omics data

Delineate outstanding genomic zones of differential gene activity

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Differential Binding Analysis of ChIP-Seq Peak Data

Differential cell-type-specific allelic imbalance

Differential Expressed Windows Based on Negative Binomial Distribution

Differential neighbourhood abundance testing on a graph

Discriminant Analysis for Evolutionary Inference

echoverse module: Annotate fine-mapping results

echoverse module: Create package dependency graphs

echoverse module: echoversePackageTitle

echoverse module: Fine-mapping data access and formatting

echoverse module: Fine-mapping functions

echoverse module: Locus plot creation for fine-mapping and colocalization studies

Empirical Analysis of Digital Gene Expression Data in R

Estimate Promoter Activity from RNA-Seq data

EWCE for Multiple Gene Lists

Exon-Intron Split Analysis (EISA) in R

Expression Weighted Celltype Enrichment

Extending guilt by association by degree

Find Causal Cell-Types Underlying Complex Trait Genetics

Find Specificity Groups with GLIPH and GLIPH2 Method

Flexible Heatmaps for Functional Genomics and Sequence Features

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Functional Gene Networks derived from biological enrichment analyses

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generation of null ranges via bootstrapping or covariate matching

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Enrichment For ChIP-seq Peak Data

Gene Set Variation Analysis for Microarray and RNA-Seq Data

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Global visualization tool of genomic data

gQTLBase: infrastructure for eQTL, mQTL and similar studies

Human Protein Atlas in R

Identification and classification of plant transcription factors

Identification of enriched motif pairs from chromatin interaction data

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

Inference And Analysis Of Synteny Networks

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

In-silico methods for genetic finemapping in inbred mice

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

interactive visualization of genomics data

Irreproducible Discovery Rate for Genomic Interactions Data

Linear Models for Microarray Data

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Locus overlap analysis for enrichment of genomic ranges

Mean Alterations Using Discrete Expression

Methylation-Based Inference of Regulatory Activity

Mining, Calling, and Importing Epigenomic Peaks in R

Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

motif matching, comparison, and de novo discovery using the MEME Suite

Multi Omic Master Regulator Analysis

Multi-Scale Target Explorer

Normalization and difference calling in ChIP-seq data

Open Reading Frames in Genomics

PatchseqMap

Perform co-DE gene analysis

preciseTAD: A machine learning framework for precise TAD boundary prediction

Preprocess epigenomic data for downstream analysis

Promoter identification from large-scale TSS profiling data

Protease Mapping

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Rapid Integration of Term Annotation and Network resources

R Interface with InterMine-Powered Databases

Rothstein Lab SGA Analysis Tools

R package for RIVER (RNA-Informed Variant Effect on Regulation)

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

R Wrapper for DGIdb

R wrapper for the OMA REST API

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

snpEva: an R package for retrieving neighboring nucleotides of an SNV

Suite of Functions for Pooled Crispr Screen QC and Analysis

Summarize, Analyze and Visualize MAF Files

Systematic quality checks on comparative genomics analyses

Tools for working with ScreenMill data

Transcript Quantification Import with Automatic Metadata

uORF prediction in R

VarCon

What the Package Does (One Line, Title Case)

Biocview "FunctionalGenomics"

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