Biocview "Visualization"

A Better Way To Explore What Is Best

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Accelerated similarity searching of small molecules

Acid Genomics Plot Functions and Themes

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Add-on of the SQUAD Software

A dynamic visualization tool of multi-level data

A Fast Scalable and Flexible Non Negative Matrix Factorization Method

Affinity test for identifying regularity Indels

Affinity test for identifying regulatory SNPs

Affymetrix Quality Assessment and Analysis Tool

A Framework for Quality Control

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

alpine

AmiGO visualize R interface

An alternative to dendrogram visualization and insertion of multiple layers of information

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing 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 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 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 sequencing data from ribosome profiling experiments

Analysis of single-cell epigenomics datasets with a Shiny App

AnaLysis routines for ePigenomicS data

Analytical Tools for MassArray Data

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

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.

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Annotation, analysis and visualization of circRNA data

Annotation and analysis of biological dynamical systems using flow cytometry

Annotation of Genomic Regions to Genomic Annotations

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 nucleosome positioning prediction

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 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 To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

An R/shiny package for microbiome functional enrichment analysis

An R toolkit for non-coding RNA

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 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 the CLIP data visualization

A package for variant peptides detection and visualization in shotgun proteomics.

A package for visualizing complex biological network

A package to plot heatmaps at different levels of a tree

A pipeline for processing drug sensitivity screen data

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 shiny GUI for MSGFplus

A small RNA-seq visualizer and analysis toolkit

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

Assessing array quality on spotted arrays

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 Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

A tool for unsupervised projection of single cell RNA-seq data

A Toolkit 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 to use GO Subtrees to Tag and Annotate Genes within a set

Augmented functionality for analysis of epigenomic variance

A universal enrichment tool for interpreting omics data

Automated analysis of high-throughput qPCR data

Automated spectraL Processing System for NMR

Automatic calculation of literature relevance of genes

A web interface for gene-set enrichment analyses

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

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.

Batch Effects Quality Control Software

Benchmarks for RNA-seq Quantification Pipelines

Big multivariate data plotted interactively

Binned Motif Enrichment Analysis and Visualization

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

Calculate growth-rate inhibition (GR) metrics

Calculate overlaps and enrichment between genomic variants and genomic features or segmentations

Calculate, visualize and analyse overlap between genomic regions

Calling aberrations for array CGH tumor profiles.

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

cell counter

Cell OrderiNg by FluorEScence Signal

cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Cheminformatics Toolkit for R

ChIPexoQual

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

Cluster and Tree Conversion.

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Clustering Comparison Package

Clustering Deviation Index (CDI)

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

CNE Detection and Visualization

Codon Usage Analysis and Prediction of Gene Expressivity

co-expressed gene-set enrichment analysis

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.

Comparative Evaluation and Visualization of Differential Expression Analyses

Compare Characteristic Features of Count Data Sets

Comparison and Visualization of Ranking and Assignment Methods

Complexome Profiling Analysis package

Compositional omics model based visual integration

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Comprehensive analysis of transciptome data

Comprehensive analysis of transcriptome data

Computational comparisons of cytometry profiles

Computation of Gene Expression-Based Signatures in Breast Cancer

Compute cell-type specific enrichments with high resolution

Condition Comparison in scRNA-seq Data

Constraint based modeling in R using metabolic reconstruction databases

Control IGB From R

Convenience package for solving some liftover challenges

Convert a Graph into a D3js Script

Convert epivizr workspaces to GViz plots, and viceversa

Coordinate-Based Genomic Visualization Package for R

CopyKit

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 prediction with correction for GC and mappability bias for HTS data

Copy Number study and Segmentation for multivariate biological data

Copy Number Visualization

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

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 Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Create Networks of Dendrochronological Series using Pairwise Similarity

Create rapid visualizations of RNAseq data in R

Creates diffusion maps

Creates hatched patterns for scatterplots

CRISPR/Cas9 gRNA designer

Crossover analysis and genetic map construction

Cross-target analysis of small molecule bioactivity

cytofast - A quick visualization and analysis tool for CyTOF data

CytofViz

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

dagLogo

dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory

dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Data analysis for cell-based functional assays

Data analysis toolkits in metagenomics

Data Management API for epiviz interactive visualization app

Data Mining and Analysis of Lipidomics Datasets

Data Package for the annoFuse Bioconductor Package

Delineate outstanding genomic zones of differential gene activity

deltaGseg

Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction

Detecting patterns of post-transcriptional modifications using machine learning

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 post-transcriptional modifications in high throughput sequencing data

Determination of essential phenotypic elements of clusters in high-dimensional entities

Development and validation of diagnostic tests from high-dimensional molecular data

dgeAnalysis

Diagnostic Plots to Evaluate the Target Decoy Approach

Differentially Expressed Gene-Gene pairs

Differentially regulated genes from scRNA-seq data

Differential Topology, Progression and Differentiation.

DiffLogo: A comparative visualisation of biooligomer motifs

Dimension Reduction for Array CGH Data with Minimal Information Loss.

Discern RNA structure proximal to protein binding

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 heatmaps in clustergrammer.js

Displaying binary trees with focus on dendrogram leaves

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 methylation data analysis and visualization

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

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis for Gene Ontology

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Epiviz Genome Browser panel for iSEEu

epiwraps: Wrappers for plotting and dealing with epigenomics data

Estimate Pairwise Interactions from multidimensional features

Evaluate Reduced Dimension Representations

Evaluation of normalization methods and calculation of differential expression analysis statistics

EWCE for Multiple Gene Lists

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

Expression data analysis via the Iterative Signature Algorithm

Expression Weighted Celltype Enrichment

FABIA: Factor Analysis for Bicluster Acquisition

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Feature-Wise Normalization for Microbiome Sequencing Data

Fingerprinting for Flow Cytometry

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Fit row-column association models with the negative binomial distribution for the microbiome

Fitting cell population growth models

Flexible Heatmaps for Functional Genomics and Sequence Features

flowPlots: analysis plots and data class for gated flow cytometry data

Functional Enrichment analysis

Functional Gene Networks derived from biological enrichment analyses

Functions for Analyzing Cellular Barcoding Data

Functions for Gene Ontology database

Functions to Access and Control Cytoscape

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

Gene Break Detection

geneChip Analysis Package

Gene expression changes in three biological conditions

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Generate PanViz visualisations from your pangenome

Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate Summary Plots of FastQC Reports

Generating SAM file for PSMs in shotgun proteomics data

Generating Tree Hierarchy Visualizations from Gene Expression Data

Generation of cell pictures

Generation of null ranges via bootstrapping or covariate matching

GeneRegionScan

Gene-Specific Phenotype EstimatoR

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Genome Level Trellis Layout

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

ggnomics

Global visualization tool of genomic data

Graph examples and use cases in Bioinformatics

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Graphical user interface for OLIN

Graphics related functions for Bioconductor

graph support for KO, KEGG Orthology

GSCA: Gene Set Context Analysis

GUI for exploratory data analysis of systems biology data

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

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

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 Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifying differential DNA loops from chromatin topology data

idiogram

igvNgl: explore relations between DNA variants and protein structure

igvR: integrative genomics viewer

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Image processing and analysis toolbox for R

Importing a tRNAscan-SE result file as GRanges object

Importing from tRNAdb and mitotRNAdb as GRanges objects

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

Integrated Analysis on two human genomic datasets

Integrated Interpretation of Genes

Integration of Disease Similarity Methods

Integrative Analysis and Visualization of Epigenomic Sequencing Data

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Interactive analysis of repeat elements

Interactive Differential Expression AnaLysis

Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Interactive HTML graphics

Interactive microbiome analysis toolkit

Interactive Multi-Omics Cancers Data Visualization and Analysis

Interactive SummarizedExperiment Explorer

Interactive visualisation of spatial proteomics data

Interactive visualization and manipulation of nested networks

Interactive Visualization for Genomic Features

interactive visualization of genomics data

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

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

IP-seq data analysis and vizualization

iSEE Universe

Iterative Differential Clustering for single-cell

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

Linear Model decomposition for Designed Multivariate Experiments

Lipidomics Analysis Tool

Main Existing Human Datasets

Make Biological Sense of Gene Set Enrichment Analysis Outputs

Make Complex Heatmaps

Make Interactive Complex Heatmaps

Make read coverage plots from BigWig files

Making 2D Hilbert Curve

Making Complex Heatmaps

Making Enriched Heatmaps

Manipulating and exploring protein and proteomics data

Mapping Alternative Splicing Events to pRoteins

mapscape

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

MicroArray Chromosome Analysis Tool

Microbial Assemblage Normalized Transcript Analysis

Microbial Community Analysis GUI

Microbiome Analysis Plotting and Visualization

Microbiome Differential Abundance Simulation

Microbiome Exploration App

mimager: The Microarray Imager

Minimized Single-Cell Consensus Clustering

Miscellaneous Functions for Metabarcoding Analysis

Mismatch Tolerant Maximum Common Substructure Searching

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

Modularized and interactive analyses over a FacileDataStore

Multi-Omics Factor Analysis (MOFA)

Multi-Omics Factor Analysis v2

Multi sample aCGH analysis package using kernel convolution

Multi-sample multi-group scRNA-seq data analysis tools

Multi-Scale Target Explorer

Multivariate Analysis of Genotype–Phenotype Association and Visualization for 3D Image

Munich ChronoType Questionnaire Tools

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data

Network Analysis for Omics Data

Network Perturbation Amplitude

Network Seriation And Modularization

Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

ontology enrichment analysis

Open-source toolkit to analyse data from xCELLigence System (RTCA)

Optimized Functional Annotation Of ChIP-seq Data

Optimized local intensity-dependent normalisation of two-color microarrays

OSAT: Optimal Sample Assignment Tool

overlapper: a shiny app to explore overlaps

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 work with miRNAs and miRNA targets with R

PatchseqMap

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

Peak saturation processing and analysis

Peptide Annotation and Data Visualization using Gviz

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

Performance Assessment and Comparison for Survival Analysis

Phenotypic EMD for comparison of single-cell samples

PhyloProfile

PhyloProfileCorona

PhyloProfileRibi

Pipeline for augmented co-expression analysis

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

Platform for integrative analysis of omics data

plot bayesian network inferred from gene expression data based on enrichment analysis results

Plot customizable linear genomes displaying arbitrary data

Plot Gene Ontology and KEGG pathway Annotation and Abundance

Plot Multiple Sequence Alignment using 'ggplot2'

Plots and annotation for choosing BrainFlow target probe sequence

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 the effect of one omics data on other omics data along the chromosome

Plotting data and annotation information along genomic coordinates

Plotting functions for derfinder

Plotting genomic information from Ensembl

PLSDA-batch

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

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 of ChIP-seq

Professional Comprehensive Omics Data Analysis

projection comparison app

Provides plotting capabilities for R graph objects

QC for enrichment based NGS

QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Quality Control for Single-Cell RNA-seq Data

Quantification and Visualization of Variations of Splicing in Population

Quantification and Visulization of Variations of Splicing in Population

Quantification of the Tumor Immune contexture from RNA-seq data

Quantile smoothing and genomic visualization of array data

Quick Read Quality Control

Randomize Samples for -omics Profiling

Rank Constrained Similarity Learning for single cell RNA sequencing data

Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Reactome Pathway Analysis

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Recipes using seqsetvis

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Refitting diploid region profiles using a clustering procedure

Regional Expression Biases

regutools: an R package for data extraction from RegulonDB

Render molecular pathways

Replicate oriented Visualization of a genomic region

Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Report of DEG analysis

Reproducible GSEA Benchmarking

Retrieve and analyze data from the Human Protein Atlas

R functions

Ribosome Profiling Quality Control

R interface to a subset of OpenBabel functionalities

R Interface to epiviz web app

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 with InterMine-Powered Databases

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

rnaSeq secondary analyses

RNA-Seq Utilities

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

rWikiPathways - R client library for the WikiPathways API

R wrapper for the python openTSNE library

Safe Color Set for Color Blindness

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

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

sechm: Complex Heatmaps from a SummarizedExperiment

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 (with hg38 and mm10).

Segvis: A package for visualization of high throughput sequencing data along genomic segments

SEPA

Set Based Visualizations for Next-Gen Sequencing Data

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 pcmp

Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Shiny-based interactive data-quality exploration for omics data

Shiny graphical interface and command-line for Regularized (or Sparse) Generalized Canonical Correlation Analysis (R/SGCCA)

Shiny interface for Cardinal

SigFuge

Similarity measures for chemical compounds

Simplified RNA-Seq Analysis Pipeline

Simplify Functional Enrichment Results

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 Consensus Clustering

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Single Cell Entropy

Single Cell Pipeline

Single Cell - R Analysis Toolbox

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

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-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

some skill for me (Title Case)

SPADE -- An analysis and visualization tool for Flow Cytometry

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

spatialHeatmap

Spatial Image Analysis of Tissues

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial Transcriptomics Analysis

Splice Interpreter of Transcripts

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 for sparse high-throughput sequencing

Statistical analysis of high-throughput RNAi screens

Statistical Analysis of Molecular Profiles

Statistical Utility for RBP (RNA binding protein) Functions

Statistics and dIagnostic Graphs for HTS

Suite of Functions for Pooled Crispr Screen QC and Analysis

Summarize, Analyze and Visualize MAF Files

Summary, annotation and visualization of genomic 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

Test and visualize gene overlaps

The Cancer Genome Atlas Data Integration

This Package Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy

This R package for performing module repertoire analyses and generating fingerprint representations

Tidy Meta Profiles using Bioconductor and the Tidyverse

Time course sequencing data analysis

Time sensitive microRNA-mRNA integration, analysis and network generation tool

TnT applications with GWAS in dn8 format

Tomo-seq data analysis

Tool for Evaluation of Cell Identity from Transcription Profiles

Tools for Actigraphy Data Analysis

Tools for Assessing Clustering

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 curating, analyzing, and manipulating biological sequences

Tools for HELP data analysis

Tools for making reports in various formats

Tools for Managing Seurat Objects

Tools for Manipulating the FOBI Ontology

Tools for microbiome analysis

Tools for Omics Data Analysis

Tools for ordering single-cell sequencing

Tools for performing taxonomic assignment.

Tools for processing of high-dimensional cytometry data

Tools for Sanger Sequencing Data in R

Tools for Single-Cell Analysis

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 Process the Munich ChronoType Questionnaire (MCTQ)

Topology-based pathway analysis of RNA-seq data

Tornado Plot

trajectory-based differential expression analysis for sequencing data

Trajectory functions for visualization and interpretation.

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

TSS sequencing data analysis

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

Unlocking iSEE for transcript-level visualization

Update Annotation to Latest Symbols using org.Hs.eq.db

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

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

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.

VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

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 quality control of large Illumina DNA Methylation array data sets

Visual Exploration of Omic Datasets Using a Shiny App

Visualise methlation data from Oxford Nanopore sequencing

Visualise methylation data from Oxford Nanopore sequencing

Visualise microarray and RNAseq data using gene ontology annotations

Visualising and Exploring Spectra Data

Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences

visualization and interpretation of textual information from omics summary data through network analysis

Visualization for flow cytometry

Visualization of Functional Enrichment Result

Visualization of high-throughput assays in microtitre plate or slide format

Visualization of Methylation Data

Visualization of multi-dimentional cancer genomics data

Visualization of Phylogenetic Networks

Visualizations for copy number alterations

Visualizations of expressionSet Bioconductor object

Visualization Tool for Genetic Reassortment

Visualization Tool for GWAS Result

Visualization Tool for Sequence Recombination and Reassortment

Visualization tools for genomic data

Visualize artificial correlation in microarray data

Visualize biclusters identified in gene expression data

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

What the Package Does (One Line, Title Case)

Word cloud summaries of GO enrichment analysis

Workflow for constructing Pathway-Gene-Transcript expression networks

Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Yet Another Package for Signature Analysis

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Yu's plot utilities

Biocview "Visualization"

R Package Documentation

Browse R Packages

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