Biocview "FunctionalGenomics"

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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
Analyze massively parallel reporter assays
Annotation of Genomic Regions to Genomic Annotations
Annotation of Genomic Regions to Genomic Annotations
An R interface to the Rfam database
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 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 analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
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 detect chromatin state switches from epigenomic data
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
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
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
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Candidate Gene Miner
Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
Cohort-scale differential expression analysis of single cell data using linear (mixed) models
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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Companion package to chipenrich
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 Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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
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-Based Genomic Visualization Package for R
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
decoupleR: Ensemble of computational methods to infer biological activities from omics data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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 Expressed Windows Based on Negative Binomial Distribution
Differential neighbourhood abundance testing on a graph
Differential neighbourhood abundance testing on a graph
Discriminant Analysis for Evolutionary Inference
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
echoverse module: Locus plot creation for fine-mapping and colocalization studies
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Estimate Promoter Activity from RNA-Seq data
Estimate Promoter Activity from RNA-Seq data
EWCE for Multiple Gene Lists
EWCE for Multiple Gene Lists
Exon-Intron Split Analysis (EISA) in R
Exon-Intron Split Analysis (EISA) in R
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Extending guilt by association by degree
Extending guilt by association by degree
Find Causal Cell-Types Underlying Complex Trait Genetics
Find Causal Cell-Types Underlying Complex Trait Genetics
Find Specificity Groups with GLIPH and GLIPH2 Method
Flexible Heatmaps for Functional Genomics and Sequence Features
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 Alternative Splicing and 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
In-silico methods for genetic finemapping in inbred mice
In-silico methods for genetic finemapping in inbred mice
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
interactive visualization of genomics data
Irreproducible Discovery Rate for Genomic Interactions Data
Irreproducible Discovery Rate for Genomic Interactions Data
Linear Models for Microarray Data
Linear Models for Microarray Data
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Mean Alterations Using Discrete Expression
Methylation-Based Inference of Regulatory Activity
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
motif matching, comparison, and de novo discovery using the MEME Suite
Multi Omic Master Regulator Analysis
Multi Omic Master Regulator Analysis
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
PatchseqMap
Perform co-DE gene analysis
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
preciseTAD: A machine learning framework for precise TAD boundary prediction
Preprocess epigenomic data for downstream analysis
Preprocess epigenomic data for downstream analysis
Promoter identification from large-scale TSS profiling data
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
Rapid Integration of Term Annotation and Network resources
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
Rothstein Lab SGA Analysis Tools
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
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 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
snpEva: an R package for retrieving neighboring nucleotides of an SNV
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Summarize, Analyze and Visualize MAF Files
Systematic quality checks on comparative genomics analyses
Test, Document, Containerise, and Deploy R Packages
Tools for working with ScreenMill data
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
uORF prediction in R
VarCon
What the Package Does (One Line, Title Case)