Biocview "Visualization"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Acid Genomics GSEA
Acid Genomics GSEA
Acid Genomics GSEA
Acid Genomics Plot Functions and Themes
Acid Genomics Plot Functions and Themes
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
Add-on of the SQUAD Software
A dynamic visualization tool of multi-level data
A dynamic visualization tool of multi-level data
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
Affinity test for identifying regulatory SNPs
Affinity test for identifying regulatory SNPs
Affymetrix Quality Assessment and Analysis Tool
A Framework for Quality Control
A Framework for Quality Control
A framework for sharing interactive data and plots from R through the web
A framework for sharing interactive data and plots from R through the web
A generic R plugin dispatcher for BASE
A gene-signature ranking method based on sample density in PCA space
A k-tables approach to integrate multiple Omics-Data
A k-tables approach to integrate multiple Omics-Data
alpine
alpine
AmiGO visualize R interface
An alternative to dendrogram visualization and insertion of multiple layers of information
An alternative to dendrogram visualization and insertion of multiple layers of information
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis of Agilent Microarray Data [draft]
Analysis of amplicon enrichment panels
Analysis of an ICA decomposition obtained on genomics data
Analysis of an ICA decomposition obtained on genomics data
Analysis of Brain Imaging Data
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 Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of cell-based screens - revised version of cellHTS
Analysis of high-throughput microscopy-based screens
Analysis of Illumina microarray data [A DRAFT - TRUE]
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analysis of sequencing data from ribosome profiling experiments
AnaLysis routines for ePigenomicS data
AnaLysis routines for ePigenomicS data
Analysis routines over a FacileDataStore
Analysis routines over a FacileDataStore
Analytical Tools for MassArray Data
Analyze flow cytometer data to determine sample ploidy
Analyze flow cytometer data to determine sample ploidy
Analyze flow cytometric data using gate information
Analyze flow cytometric data using histogram information
Analyzing tRNA sequences and structures
Analyzing tRNA sequences and structures
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
Annotation, analysis and visualization of circRNA data
Annotation and analysis of biological dynamical systems using flow cytometry
Annotation and analysis of biological dynamical systems using flow cytometry
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 Adjusting Bias in Gene Set Enrichment Analysis
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
An R package for nucleosome positioning prediction
An R package for proteomics data quality control
An R package for proteomics data quality control
An R package for qualitative biclustering in support of gene co-expression analyses
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 retrieving data from DAVID into R objects using Web Services API.
An R package for RNA visualization and analysis
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
An R package for useful bioinformatics wrappers
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
an R package for visualization of tree and annotation data
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for nonlinear dimension reduction with Isomap and LLE.
A package for nonlinear dimension reduction with Isomap and LLE.
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
A package for variant peptides detection and visualization in shotgun proteomics.
A package for visualizing complex biological network
Application of t-sne to NGS Genomic Signal Profiles
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A shiny GUI for MSGFplus
A small RNA-seq visualizer and analysis toolkit
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
Assess Gene Predictions Using Proteomics and Evolutionary Conservation
Assessing array quality on spotted arrays
A SummarizedExperiment for Ivy-GAP data
A SummarizedExperiment for Ivy-GAP data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations.
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A Toolkit for Flow And Mass Cytometry Data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
Augmented functionality for analysis of epigenomic variance
Automated analysis of high-throughput qPCR data
Automated spectraL Processing System for NMR
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
A web interface for gene-set enrichment analyses
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic graphic utilities for visualization of genomic data.
Basic graphic utilities for visualization of genomic data.
Batch Effects Quality Control Software
bcbio RNA-Seq
bcbio RNA-Seq
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Brain Span Atlas in Biobase Expressionset R toolset
Broadcast data between R and Gaggle
BrowserHeatmap: a BrowserViz subclass for displaying heatmaps
BrowserVizDemo2: How to add a feature to BrowserVizDemo
BrowserVizDemo: How to subclass BrowserViz
BrowserViz: interactive R/browser graphics using websockets and JSON
BrowserViz: interactive R/browser graphics using websockets and JSON
Calculate growth-rate inhibition (GR) metrics
Calculate growth-rate inhibition (GR) metrics
Calculate growth-rate inhibition (GR) metrics
Calculate overlaps and enrichment between genomic variants and genomic features or segmentations
Calling aberrations for array CGH tumor profiles.
Calling aberrations for array CGH tumor profiles.
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
cell counter
Cell OrderiNg by FluorEScence Signal
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
ChIPexoQual
ChIPexoQual
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Clonal ordering and visualization
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Cluster and Tree Conversion.
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering Comparison Package
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering for Flow Cytometry
Clustering for Flow Cytometry
CNE Detection and Visualization
CNE Detection and Visualization
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
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.
Compare Characteristic Features of Count Data Sets
Compare Characteristic Features of Count Data Sets
Compositional omics model based visual integration
Compositional omics model based visual integration
Compositional omics model based visual integration
Comprehensive analysis of transciptome data
Comprehensive analysis of transcriptome data
Computational comparisons of cytometry profiles
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Compute cell-type specific enrichments with high resolution
Condition Comparison in scRNA-seq Data
Condition Comparison in scRNA-seq Data
Constraint based modeling in R using metabolic reconstruction databases
Constraint based modeling in R using metabolic reconstruction databases
Control IGB From R
Convenience package for solving some liftover challenges
Convenience package for solving some liftover challenges
Convert a Graph into a D3js Script
Convert epivizr workspaces to GViz plots, and viceversa
Convert epivizr workspaces to GViz plots, and viceversa
Convert epivizr workspaces to GViz plots, and viceversa
Copy number information from ChIP_seq using off-target reads off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy Number study and Segmentation for multivariate biological data
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Correspondence Analysis for Single Cell Data
Coverage visualization package for R
Create Copy-Number Plots using karyoploteR functionality
Create Copy-Number Plots using karyoploteR functionality
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Creates diffusion maps
Creates diffusion maps
CRISPR/Cas9 gRNA designer
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
cytofast - A quick visualization and analysis tool for CyTOF data
cytofast - A quick visualization and analysis tool for CyTOF data
CytofViz
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
dagLogo
dagLogo
dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory
dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory
Data analysis for cell-based functional assays
Data Management API for epiviz interactive visualization app
Data Management API for epiviz interactive visualization app
Data Mining and Analysis of Lipidomics Datasets
Data Mining and Analysis of Lipidomics Datasets
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
deltaGseg
DESeq2 Analysis Utilities
DESeq2 Analysis Utilities
Detecting patterns of post-transcriptional modifications using machine learning
Detecting patterns of post-transcriptional modifications using machine learning
Detection of 2'-O methylations by RiboMethSeq
Detection of 2'-O methylations by RiboMethSeq
Detection of focal aberrations in DNA copy number data
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of m7G, m3C and D modification by AlkAnilineSeq
Detection of post-transcriptional modifications in high throughput sequencing data
Detection of post-transcriptional modifications in high throughput sequencing data
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Development and validation of diagnostic tests from high-dimensional molecular data
dgeAnalysis
DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo: A comparative visualisation of biooligomer motifs
Dimension Reduction for Array CGH Data with Minimal Information Loss.
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Display and manipulate graphs in Cytoscape
Display and manipulate graphs in Cytoscape >= 3.3.0
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in cytoscape.js
Display and manipulate graphs in cytoscape.js
Display and manipulate heatmaps in clustergrammer.js
distinct: a method for differential analyses via hierarchical permutation tests
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA methylation data analysis and visualization
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
Efficient compression and analysis of Hi-C Data
Empirical Bayesian approach to mutational signature discovery
Empirical Bayesian approach to mutational signature discovery
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enrichment Analysis for Gene Ontology
Enrichment Analysis for Gene Ontology
Estimate Pairwise Interactions from multidimensional features
Evaluate Reduced Dimension Representations
Evaluation of normalization methods and calculation of differential expression analysis statistics
Evaluation of normalization methods and calculation of differential expression analysis statistics
Exploration and Significant Biology on a Gene Set.
Exploratory analysis and differential expression for RNA-seq data
Explores single cell copy number profiles in the context of a single cell tree
Export plotting files to the xmapBridge for visualisation in X:Map
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration analysis
Expression data analysis via the Iterative Signature Algorithm
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
FABIA: Factor Analysis for Bicluster Acquisition
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Fingerprinting for Flow Cytometry
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Fit row-column association models with the negative binomial distribution for the microbiome
Fit row-column association models with the negative binomial distribution for the microbiome
Fitting cell population growth models
Fitting cell population growth models
Flexible Heatmaps for Functional Genomics and Sequence Features
Flexible Heatmaps for Functional Genomics and Sequence Features
flowPlots: analysis plots and data class for gated flow cytometry data
Functional Enrichment analysis
Functional Enrichment analysis
Functional Gene Networks derived from biological enrichment analyses
Functions for Gene Ontology database
Functions to Access and Control Cytoscape
Functions to Access and Control Cytoscape
Functions to help analyze data as phyloseq objects
Functions to help analyze data as phyloseq objects
Functions to perform cancer outlier profile analysis.
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Gene Break Detection
geneChip Analysis Package
Gene expression changes in three biological conditions
Gene expression changes in three biological conditions
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate PanViz visualisations from your pangenome
Generate PanViz visualisations from your pangenome
Generate Summary Plots of FastQC Reports
Generating SAM file for PSMs in shotgun proteomics data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
GeneRegionScan
Gene-Specific Phenotype EstimatoR
Gene-Specific Phenotype EstimatoR
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Genome Level Trellis Layout
Genome Level Trellis Layout
Genome Level Trellis Layout
Global visualization tool of genomic data
Graph examples and use cases in Bioinformatics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical user interface for OLIN
Graphics related functions for Bioconductor
Graphics related functions for Bioconductor
graph support for KO, KEGG Orthology
GSCA: Gene Set Context Analysis
GSCA: Gene Set Context Analysis
GSCA: Gene Set Context Analysis
GUI for exploratory data analysis of systems biology data
GUI for exploratory data analysis of systems biology data
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
Handling Missing Individuals in Multi-Omics Data Integration
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
Heat map plotting by genome coordinate
Heatmaps with row and/or column covariates and colored clusters
Heatmaps with row and/or column covariates and colored clusters
Hexbin plots for single cell omics data
Hexbin plots for single cell omics data
Hi-C Annotation and Graphics Ensemble
High-quality circular visualization of omics data
High-Throughput Sequence Analysis using the Aroma Framework
Hilbert curve visualization
HilbertVisGUI
Hits Selection for Synthetic Lethal RNAi Screen Data
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Identifies false positives of CNV calling tools by using SNV calls
Identifies false positives of CNV calling tools by using SNV calls
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.
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
idiogram
igvNgl: explore relations between DNA variants and protein structure
igvR: integrative genomics viewer
igvR: integrative genomics viewer
igvR: integrative genomics viewer
igvR: integrative genomics viewer
ILoReg enables high-precision cell population identification from scRNA-Seq data
Image processing and analysis toolbox for R
Image processing and analysis toolbox for R
Importing a tRNAscan-SE result file as GRanges object
Importing a tRNAscan-SE result file as GRanges object
Importing a tRNAscan-SE result file as GRanges object
Importing from tRNAdb and mitotRNAdb as GRanges objects
Importing from tRNAdb and mitotRNAdb as GRanges objects
Improving replicability in single-cell RNA-Seq cell type discovery
Improving replicability in single-cell RNA-Seq cell type discovery
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Integrated Analysis on two human genomic datasets
Integrated Analysis on two human genomic datasets
Integrated Interpretation of Genes
Integration of Disease Similarity Methods
Integration of Disease Similarity Methods
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Interactive analysis of repeat elements
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interactive HTML graphics
Interactive HTML graphics
Interactive microbiome analysis toolkit
Interactive microbiome analysis toolkit
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive visualisation of spatial proteomics data
Interactive visualisation of spatial proteomics data
Interactive visualization and manipulation of nested networks
Interactive Visualization for Genomic Features
Interactive Visualization for Genomic Features
interactive visualization of genomics data
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive visualization of scRNA-seq data with Cerebro
Interactive Workflow for Discovering Rhythmicity in Biological Data
Interactive Workflow for Discovering Rhythmicity in Biological Data
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
iSEE Universe
iSEE Universe
iSEE Universe
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KMPPc: K-M Plot for Pan-cancer
Landscape Single Cell Entropy
Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Linear Model decomposition for Designed Multivariate Experiments
Lipidomics Analysis Tool
Make Complex Heatmaps
Make Complex Heatmaps
Make Complex Heatmaps
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Make Sense to Gene Set Enrichment Analysis Outputs
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making Complex Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Mapping Alternative Splicing Events to pRoteins
Mapping Alternative Splicing Events to pRoteins
mapscape
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Matched Interaction across Tissues (MIxT) data analysis
MBDDiff for processing MBDcap-seq datasets
Merge Maid
Merging of phenotype information from different cytometric profiles
Meta-data and tools for E. coli
MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
Methods for Continuous Flow Cytometry
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
MicroArray Chromosome Analysis Tool
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Microbial Community Analysis GUI
Microbiome Differential Abundance Simulation
microRNA-mRNA Integration, Analysis and Network Generation Tool
mimager: The Microarray Imager
mimager: The Microarray Imager
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Model-View-Controller (MVC) Classes
Model-View-Controller (MVC) Classes That Use Biobase
Multi-Omics Factor Analysis (MOFA)
Multi-Omics Factor Analysis (MOFA)
Multi sample aCGH analysis package using kernel convolution
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multivariate Analysis of Genotype–Phenotype Association and Visualization for 3D Image
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data
Network Perturbation Amplitude
Network Perturbation Amplitude
Network Seriation And Modularization
ontology enrichment analysis
Open-source toolkit to analyse data from xCELLigence System (RTCA)
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized local intensity-dependent normalisation of two-color microarrays
OSAT: Optimal Sample Assignment Tool
OSAT: Optimal Sample Assignment Tool
overlapper: a shiny app to explore overlaps
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Package for enabling powerful shiny web displays of Bioconductor objects
Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling
Package for Single-cell Data Visualization and Analysis
Package to Draw Protein Schematics from Uniprot API output
Package to Draw Protein Schematics from Uniprot API output
Package to work with miRNAs and miRNA targets with R
PatchseqMap
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Patient Clonal Timescapes
patternCNV: a versatile tool for detecting copy number changes from exome-seq data
pcaGoPromoter is used to analyze DNA micro array data
Peptide Annotation and Data Visualization using Gviz
Peptide Annotation and Data Visualization using Gviz
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
PhyloProfile
PhyloProfile
PhyloProfile
Pipeline for augmented co-expression analysis
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Plots and annotation for choosing BrainFlow target probe sequence
Plots and annotation for choosing BrainFlow target probe sequence
Plots data (continuous/discrete) along chromosomal ideogram
Plots data (continuous/discrete) along chromosomal ideogram
Plots of Statistics Collected by Qualimap from RNASeq Data
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot the effect of one omics data on other omics data along the chromosome
Plot the effect of one omics data on other omics data along the chromosome
Plotting data and annotation information along genomic coordinates
Plotting data and annotation information along genomic coordinates
Plotting functions for derfinder
Plotting functions for derfinder
Plotting genomic information from Ensembl
PolyA counting and differential transcript usage analysis for scRNA-seq data
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Pre-process 1H-NMR FID signals
Preprocessing of GC-MS metabolomics data with a GUI and interactive plots.
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Produces Summaries and Plots of Features Distributed Across Genomes
projection comparison app
Provides plotting capabilities for R graph objects
Provides plotting capabilities for R graph objects
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantile smoothing and genomic visualization of array data
Quick Read Quality Control
Quick Read Quality Control
R/Bioconductor package to manage hierarchies in genomic datasets
R/Bioconductor package to manage hierarchies in genomic datasets
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Reactome Pathway Analysis
Reactome Pathway Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Recipes using seqsetvis
Regional Expression Biases
regutools: an R package for data extraction from RegulonDB
Render molecular pathways
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Report of DEG analysis
Report of DEG analysis
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
Retrieve and analyze data from the Human Protein Atlas
Retrieve and analyze data from the Human Protein Atlas
R functions
RGCCA and Sparse GCCA for multi-block data analysis
Ribosome Profiling Quality Control
Ribosome Profiling Quality Control
R interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R Interface to epiviz web app
R Interface to epiviz web app
R Interface to epiviz web app
R Interface to epiviz web app
R interface to epiviz web components
R interface to epiviz web components
R interface to epiviz web components
R interface to epiviz web components
R interface to genome annotation files and the UCSC genome browser
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
R package for Manhattan Plots
R package for Manhattan Plots
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
R package motivated by the SCTC Dream Challenges
Run Epiviz Interactive Genomic Data Visualization App within R
Run Epiviz Interactive Genomic Data Visualization App within R
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
rWikiPathways - R client library for the WikiPathways API
Safe Color Set for Color Blindness
Safe Color Set for Color Blindness
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless visualization of complex genomic variations in GMOs and edited cell lines
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Segmentation of single- and multi-track copy number data by penalized least squares regression.
Segvis: A package for visualization of high throughput sequencing data along genomic segments
SEPA
SEPA
Set Based Visualizations for Next-Gen Sequencing Data
Set Based Visualizations for Next-Gen Sequencing Data
SEtools: tools for working with SummarizedExperiment
SEtools: tools for working with SummarizedExperiment
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
shiny app for pcmp
Shiny interface for Cardinal
SigFuge
SigFuge
Similarity measures for chemical compounds
Simplified RNA-Seq Analysis Pipeline
Simplify Functional Enrichment Results
Simplify Functional Enrichment Results
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-cell RNA-seq toolkit
Single-cell RNA-seq toolkit
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Single Molecule Localization Microscopy visualization and analysis in R
Single Molecule Localization Microscopy visualization and analysis in R
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
small RNA-Seq Utilities
Soft clustering of time series gene expression data
Somatic Signatures
Somatic Signatures
Somatic Signatures
some skill for me (Title Case)
SPADE -- An analysis and visualization tool for Flow Cytometry
SPADE -- An analysis and visualization tool for Flow Cytometry
SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
Splice Interpreter of Transcripts
Splice Interpreter of Transcripts
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis of high-throughput RNAi screens
Statistical Analysis of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistics and dIagnostic Graphs for HTS
Statistics and dIagnostic Graphs for HTS
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
Summary, annotation and visualization of genomic data
Summary, annotation and visualization of genomic data
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Test and visualize gene overlaps
Test and visualize gene overlaps
The Cancer Genome Atlas Data Integration
Tidy Meta Profiles using Bioconductor and the Tidyverse
Time course sequencing data analysis
Time course sequencing data analysis
Tool for Evaluation of Cell Identity from Transcription Profiles
Tool for Evaluation of Cell Identity from Transcription Profiles
Tools for computational epigenomics
Tools for computational epigenomics
Tools for computing, querying and storing linkage-disequilibrium data
Tools for counting and visualising mutations in a target location
Tools for counting and visualising mutations in a target location
Tools for counting and visualising mutations in a target location
Tools for curating, analyzing, and manipulating biological sequences
Tools for HELP data analysis
Tools for making reports in various formats
Tools for making reports in various formats
Tools for microbiome analysis
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for performing taxonomic assignment.
Tools for processing of high-dimensional cytometry data
Tools for processing of high-dimensional cytometry data
Tools for Sanger Sequencing Data in R
Tools for visualizing genomics data
Tools for visualizing genomics data
tools for working with cell fate maps
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells.
Topology-based pathway analysis of RNA-seq data
Topology-based pathway analysis of RNA-seq data
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcript mapping with high-density oligonucleotide tiling arrays
TrenaViz
trenaViz: network and genome track visualization for trena
TSCAN: Tools for Single-Cell ANalysis
TSCAN: Tools for Single-Cell ANalysis
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Update Annotation to Latest Symbols using org.Hs.eq.db
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
Using self-organizing maps for visualization and interpretation of cytometry data
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.
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.
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
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences
Visualization for flow cytometry
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of high-throughput assays in microtitre plate or slide format
Visualization of multi-dimentional cancer genomics data
Visualization of multi-dimentional cancer genomics data
Visualization of Phylogenetic Networks
Visualization of Phylogenetic Networks
Visualizations for copy number alterations
Visualizations of expressionSet Bioconductor object
Visualization Tool for Sequence Recombination and Reassortment
Visualization Tool for Sequence Recombination and Reassortment
Visualization tools for genomic data
Visualization tools for genomic data
Visualize artificial correlation in microarray data
Visualize biclusters identified in gene expression data
Visualize Cytometry data with ggplot
Visualize Cytometry data with ggplot
visualize genome-wide association study with gene annotation and linkage disequiblism
Visualizing Hypergaphs
Visualizing Structure in ecological site-species abundance data
WebSocket server infrastructure for epivizr apps and packages
WebSocket server infrastructure for epivizr apps and packages
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
Word cloud summaries of GO enrichment analysis
Word cloud summaries of GO enrichment analysis
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yet Another Package for Signature Analysis
Yu's plot utilities