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 CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analyze massively parallel reporter assays
Analyze massively parallel reporter assays
Annotation of Genomic Regions to Genomic Annotations
Annotation of Genomic Regions to Genomic Annotations
Annotation of Genomic Regions to Genomic Annotations
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
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 Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Isoform Switches with Functional Consequences (from RNA-seq data)
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
Basic peak calling on STARR-seq data
Basic peak calling on STARR-seq data
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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Companion package to chipenrich
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
Coordinate Covariation Analysis
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
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Extending guilt by association by degree
Extending guilt by association by degree
Extending guilt by association by degree
Flexible Heatmaps for Functional Genomics and Sequence Features
Flexible Heatmaps for Functional Genomics and Sequence Features
Functional Gene Networks derived from biological enrichment analyses
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
Gene Set Enrichment For ChIP-seq Peak Data
Gene Set Enrichment For ChIP-seq Peak Data
Global visualization tool of genomic data
Global visualization tool of genomic data
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLBase: infrastructure for eQTL, mQTL and similar studies
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative analysis pipeline for pooled CRISPR functional genetic screens
interactive visualization of genomics data
Location overlap analysis for enrichment of genomic ranges
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
MAGMA.Celltyping
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
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
PatchseqMap
Principal Component Region Set Analysis
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Rapid Integration of Term Annotation and Network resources
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 RIVER (RNA-Informed Variant Effect on Regulation)
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
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 DGIdb
R wrapper for the OMA REST API
R wrapper for the OMA REST API
R wrapper for the OMA REST API
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
Tools for working with ScreenMill data