Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "Visualization" keyword

multistateQTL 1.0.0
Toolkit for the analysis of multi-state QTL data
1 version - Latest release: about 1 month ago - 197 downloads total - 0 stars on GitHub - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 26 days ago - 5.05 thousand downloads total - 13 stars on GitHub - 1 maintainer
mosdef 1.0.0
MOSt frequently used and useful Differential Expression Functions
1 version - Latest release: about 1 month ago - 0 stars on GitHub - 1 maintainer
spillR 0.99.10
Spillover Compensation in Mass Cytometry Data
2 versions - Latest release: about 1 month ago - 392 downloads total - 1 maintainer
Top 5.5% on bioconductor.org
iSEE 2.16.0
Interactive SummarizedExperiment Explorer
3 versions - Latest release: about 1 month ago - 8 dependent packages - 34.1 thousand downloads total - 220 stars on GitHub - 1 maintainer
PLSDAbatch 1.0.0
PLSDA-batch
1 version - Latest release: about 1 month ago - 417 downloads total - 11 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance
1 version - Latest release: about 1 month ago - 295 downloads total - 0 stars on GitHub - 1 maintainer
gINTomics 1.0.0
Multi-Omics data integration
1 version - Latest release: about 1 month ago - 128 downloads total - 3 stars on GitHub - 1 maintainer
shiny.gosling 1.0.0
A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny
2 versions - Latest release: about 1 month ago - 1 dependent package - 426 downloads total - 1 maintainer
mobileRNA 1.0.0
mobileRNA: Investigate the RNA mobilome & population-scale changes
2 versions - Latest release: about 1 month ago - 405 downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.24.0
Visualization of Functional Enrichment Result
3 versions - Latest release: 30 days ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: 30 days ago - 96 dependent packages - 625 thousand downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data
4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.12.0
an R package for visualization of tree and annotation data
4 versions - Latest release: 30 days ago - 28 dependent packages - 1.16 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.48.0
Provides plotting capabilities for R graph objects
3 versions - Latest release: 30 days ago - 61 dependent packages - 1.52 million downloads total - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.64.0
R interface to genome annotation files and the UCSC genome browser
3 versions - Latest release: 30 days ago - 251 dependent packages - 3.88 million downloads total - 1 maintainer
MICSQTL 1.0.0
MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
2 versions - Latest release: 7 months ago - 1.03 thousand downloads total - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis
3 versions - Latest release: 7 months ago - 17.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
iSEEpathways 1.0.0
iSEE extension for panels related to pathway analysis
2 versions - Latest release: 7 months ago - 1.03 thousand downloads total - 1 stars on GitHub - 1 maintainer
QUBIC 1.30.0
An R package for qualitative biclustering in support of gene co-expression analyses
3 versions - Latest release: 6 months ago - 2 dependent packages - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
tRNAscanImport 1.22.0
Importing a tRNAscan-SE result file as GRanges object
3 versions - Latest release: 6 months ago - 2 dependent packages - 7.99 thousand downloads total - 2 stars on GitHub - 1 maintainer
distinct 1.14.5
distinct: a method for differential analyses via hierarchical permutation tests
4 versions - Latest release: 5 months ago - 2 dependent packages - 8.74 thousand downloads total - 11 stars on GitHub - 1 maintainer
SARC 1.0.0
Statistical Analysis of Regions with CNVs
2 versions - Latest release: 7 months ago - 933 downloads total - 0 stars on GitHub - 1 maintainer
BioCartaImage 1.0.0
BioCarta Pathway Images
2 versions - Latest release: 7 months ago - 996 downloads total - 10 stars on GitHub - 1 maintainer
DiffLogo 2.26.0
DiffLogo: A comparative visualisation of biooligomer motifs
3 versions - Latest release: 7 months ago - 12.8 thousand downloads total - 7 stars on GitHub
igvR 1.22.0
igvR: integrative genomics viewer
3 versions - Latest release: 7 months ago - 11.6 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.32.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
3 versions - Latest release: 7 months ago - 5 dependent packages - 50.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
TimiRGeN 1.11.0
Time sensitive microRNA-mRNA integration, analysis and network generation tool
3 versions - Latest release: 7 months ago - 1 dependent package - 3.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files
3 versions - Latest release: about 1 month ago - 9 dependent packages - 227 thousand downloads total - 423 stars on GitHub - 1 maintainer
animalcules 1.18.3
Interactive microbiome analysis toolkit
5 versions - Latest release: 3 months ago - 8.8 thousand downloads total - 50 stars on GitHub - 1 maintainer
limpca 1.0.0
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family ...
1 version - Latest release: about 1 month ago - 192 downloads total - 0 stars on GitHub - 1 maintainer
InterCellar 2.8.0
InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication i...
3 versions - Latest release: 6 months ago - 4.35 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
ChemmineR 3.54.0
Cheminformatics Toolkit for R
3 versions - Latest release: 7 months ago - 8 dependent packages - 482 thousand downloads total - 13 stars on GitHub - 1 maintainer
geneXtendeR 1.28.0
Optimized Functional Annotation Of ChIP-seq Data
3 versions - Latest release: 6 months ago - 13.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
CCPlotR 1.0.0
Plots For Visualising Cell-Cell Interactions
2 versions - Latest release: 7 months ago - 1.09 thousand downloads total - 22 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App
3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
CytoPipeline 1.4.0
Automation and visualization of flow cytometry data analysis pipelines
3 versions - Latest release: 23 days ago - 2 dependent packages - 1.97 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
annotatr 1.28.0
Annotation of Genomic Regions to Genomic Annotations
3 versions - Latest release: 6 months ago - 6 dependent packages - 58.4 thousand downloads total - 25 stars on GitHub - 1 maintainer
TSAR 1.0.0
Thermal Shift Analysis in R
2 versions - Latest release: 7 months ago - 913 downloads total - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations
3 versions - Latest release: 6 months ago - 1 dependent package - 24.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
biovizBase 1.50.0
Basic graphic utilities for visualization of genomic data.
3 versions - Latest release: 7 months ago - 17 dependent packages - 1.05 million downloads total - 1 maintainer
RNAmodR 1.16.0
Detection of post-transcriptional modifications in high throughput sequencing data
3 versions - Latest release: 7 months ago - 3 dependent packages - 6.93 thousand downloads total - 2 stars on GitHub - 1 maintainer
RNAmodR.AlkAnilineSeq 1.16.0
Detection of m7G, m3C and D modification by AlkAnilineSeq
3 versions - Latest release: 6 months ago - 1 dependent package - 5.39 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.46.0
Reactome Pathway Analysis
3 versions - Latest release: 7 months ago - 15 dependent packages - 443 thousand downloads total - 1 maintainer
SPLINTER 1.28.0
Splice Interpreter of Transcripts
3 versions - Latest release: 7 months ago - 10.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
ncRNAtools 1.12.0
An R toolkit for non-coding RNA
3 versions - Latest release: 6 months ago - 3.66 thousand downloads total - 1 stars on GitHub - 1 maintainer
vidger 1.22.0
Create rapid visualizations of RNAseq data in R
3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
ggbio 1.50.0
Visualization tools for genomic data
4 versions - Latest release: 7 months ago - 27 dependent packages - 443 thousand downloads total - 110 stars on GitHub - 1 maintainer
GWENA 1.12.0
Pipeline for augmented co-expression analysis
3 versions - Latest release: 6 months ago - 7.57 thousand downloads total - 18 stars on GitHub - 1 maintainer
HilbertCurve 1.32.0
Making 2D Hilbert Curve
3 versions - Latest release: 6 months ago - 1 dependent package - 15.8 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.40.0
Base package for enabling powerful shiny web displays of Bioconductor objects
3 versions - Latest release: 7 months ago - 3 dependent packages - 802 thousand downloads total - 1 maintainer
cardelino 1.4.0
Clone Identification from Single Cell Data
3 versions - Latest release: 7 months ago - 2.53 thousand downloads total - 54 stars on GitHub - 1 maintainer
motifbreakR 2.16.0
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription F...
3 versions - Latest release: 6 months ago - 20.3 thousand downloads total - 24 stars on GitHub - 1 maintainer
PepsNMR 1.20.0
Pre-process 1H-NMR FID signals
3 versions - Latest release: 6 months ago - 1 dependent package - 9.18 thousand downloads total - 10 stars on GitHub - 1 maintainer
annmap 1.44.0
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
3 versions - Latest release: 6 months ago - 19.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
SomaticSignatures 2.38.0
Somatic Signatures
3 versions - Latest release: 6 months ago - 1 dependent package - 43.5 thousand downloads total - 21 stars on GitHub - 1 maintainer
lipidr 2.16.0
Data Mining and Analysis of Lipidomics Datasets
3 versions - Latest release: 6 months ago - 1 dependent package - 10.2 thousand downloads total - 25 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
ComplexHeatmap 2.18.0
Make Complex Heatmaps
3 versions - Latest release: 7 months ago - 101 dependent packages - 1.04 million downloads total - 21 stars on GitHub - 1 maintainer
microbiomeDASim 1.16.0
Microbiome Differential Abundance Simulation
3 versions - Latest release: 6 months ago - 4.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
CytoPipelineGUI 1.0.0
GUI's for visualization of flow cytometry data analysis pipelines
2 versions - Latest release: 7 months ago - 921 downloads total - 0 stars on GitHub - 1 maintainer
tomoda 1.12.0
Tomo-seq data analysis
3 versions - Latest release: 6 months ago - 3.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
Director 1.28.0
A dynamic visualization tool of multi-level data
3 versions - Latest release: 6 months ago - 8.62 thousand downloads total - 0 stars on GitHub - 1 maintainer
simplifyEnrichment 1.12.0
Simplify Functional Enrichment Results
3 versions - Latest release: 6 months ago - 4 dependent packages - 23.2 thousand downloads total - 96 stars on GitHub - 1 maintainer
SGCP 1.2.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
3 versions - Latest release: 7 months ago - 1.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
bioassayR 1.40.0
Cross-target analysis of small molecule bioactivity
3 versions - Latest release: 6 months ago - 24.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
topGO 2.54.0
Enrichment Analysis for Gene Ontology
3 versions - Latest release: 7 months ago - 26 dependent packages - 462 thousand downloads total - 1 maintainer
HPAanalyze 1.20.0
Retrieve and analyze data from the Human Protein Atlas
3 versions - Latest release: 6 months ago - 9.03 thousand downloads total - 27 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.62.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
3 versions - Latest release: 7 months ago - 13 dependent packages - 541 thousand downloads total - 1 maintainer
ILoReg 1.12.1
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
4 versions - Latest release: 3 months ago - 3.61 thousand downloads total - 4 stars on GitHub - 1 maintainer
cummeRbund 2.44.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
3 versions - Latest release: 7 months ago - 576 thousand downloads total - 1 maintainer
CAGEfightR 1.22.0
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
3 versions - Latest release: 6 months ago - 1 dependent package - 18.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
scruff 1.20.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 8 stars on GitHub - 1 maintainer
transcriptogramer 1.24.0
Transcriptional analysis based on transcriptograms
3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.36.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
3 versions - Latest release: 6 months ago - 1 dependent package - 24.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
geneplotter 1.80.0
Graphics related functions for Bioconductor
3 versions - Latest release: 7 months ago - 9 dependent packages - 2.3 million downloads total - 1 maintainer
OGRE 1.6.0
Calculate, visualize and analyse overlap between genomic regions
3 versions - Latest release: 6 months ago - 2.13 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
Nebulosa 1.12.1
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
4 versions - Latest release: 2 months ago - 36.7 thousand downloads total - 63 stars on GitHub - 1 maintainer
MBECS 1.6.0
Evaluation and correction of batch effects in microbiome data-sets
3 versions - Latest release: 6 months ago - 2.63 thousand downloads total - 4 stars on GitHub - 1 maintainer
gg4way 1.0.2
4way Plots of Differential Expression
4 versions - Latest release: 3 months ago - 983 downloads total - 0 stars on GitHub - 1 maintainer
flowPloidy 1.28.0
Analyze flow cytometer data to determine sample ploidy
3 versions - Latest release: 7 months ago - 10.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
gtrellis 1.34.0
Genome Level Trellis Layout
3 versions - Latest release: 6 months ago - 1 dependent package - 21.9 thousand downloads total - 39 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data
6 versions - Latest release: 3 months ago - 2.37 thousand downloads total - 8 stars on GitHub - 1 maintainer
RNAinteract 1.50.0
Estimate Pairwise Interactions from multidimensional features
3 versions - Latest release: 7 months ago - 23.7 thousand downloads total - 1 maintainer
InteractiveComplexHeatmap 1.10.0
Make Interactive Complex Heatmaps
3 versions - Latest release: 7 months ago - 4 dependent packages - 15.6 thousand downloads total - 112 stars on GitHub - 1 maintainer
DESpace 1.2.1
DESpace: a framework to discover spatially variable genes
4 versions - Latest release: 3 months ago - 1.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
UMI4Cats 1.12.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
3 versions - Latest release: 7 months ago - 3.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
GDCRNATools 1.22.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...
3 versions - Latest release: 7 months ago - 36.3 thousand downloads total - 2 maintainers
maser 1.20.0
Mapping Alternative Splicing Events to pRoteins
3 versions - Latest release: 7 months ago - 10.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering
3 versions - Latest release: 7 months ago - 1.7 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
macat 1.76.0 removed
MicroArray Chromosome Analysis Tool
2 versions - Latest release: 7 months ago - 29.9 thousand downloads total - 1 maintainer
schex 1.16.1
Hexbin plots for single cell omics data
4 versions - Latest release: 4 months ago - 3 dependent packages - 13.8 thousand downloads total - 71 stars on GitHub - 1 maintainer
Basic4Cseq 1.38.0
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
3 versions - Latest release: 7 months ago - 20.6 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App
3 versions - Latest release: 7 months ago - 6.29 thousand downloads total - 1 maintainer
abseqR 1.20.0
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
3 versions - Latest release: 7 months ago - 7.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data
3 versions - Latest release: 7 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
rGenomeTracks 1.8.0
Integerated visualization of epigenomic data
3 versions - Latest release: 7 months ago - 2.13 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
RTCA 1.54.0
Open-source toolkit to analyse data from xCELLigence System (RTCA)
3 versions - Latest release: 7 months ago - 26.5 thousand downloads total - 1 maintainer
mapscape 1.26.0
mapscape
3 versions - Latest release: 7 months ago - 8.41 thousand downloads total - 1 maintainer
NanoMethViz 2.8.1
Visualise methylation data from Oxford Nanopore sequencing
3 versions - Latest release: 7 months ago - 5.55 thousand downloads total - 20 stars on GitHub - 1 maintainer
Related Keywords
Software 433 Sequencing 134 GeneExpression 115 RNASeq 97 ImmunoOncology 93 Clustering 89 DifferentialExpression 73 Microarray 64 QualityControl 63 SingleCell 61 DataImport 59 Preprocessing 54 MultipleComparison 51 Transcriptomics 49 DataRepresentation 43 GeneSetEnrichment 43 Annotation 43 Transcription 42 Genetics 35 r 35 bioconductor 35 GUI 35 Coverage 34 CellBasedAssays 34 GraphAndNetwork 33 DimensionReduction 33 Pathways 33 Normalization 32 Infrastructure 31 Proteomics 31 Network 26 StatisticalMethod 25 GO 25 Classification 25 FunctionalGenomics 23 FlowCytometry 23 ReportWriting 22 CopyNumberVariation 21 ChIPSeq 21 Metabolomics 20 PrincipalComponent 20 ShinyApps 19 Alignment 17 BiomedicalInformatics 16 AlternativeSplicing 16 KEGG 16 Microbiome 15 bioinformatics 15 MassSpectrometry 15 SystemsBiology 15 BatchEffect 14 DNASeq 13 WorkflowStep 13 Spatial 13 Regression 13 CellBiology 13 GenomeAnnotation 13 DNAMethylation 12 GeneTarget 12 TimeCourse 12 FeatureExtraction 11 Bayesian 10 Metagenomics 10 rstats 10 GeneRegulation 10 SequenceMatching 10 ThirdPartyClient 10 ExperimentalDesign 10 Epigenetics 9 OneChannel 9 NetworkEnrichment 9 DifferentialSplicing 9 MicrotitrePlateAssay 9 Reactome 8 TwoChannel 8 shiny 8 GenomicVariation 8 DifferentialMethylation 8 GeneticVariability 7 MotifAnnotation 7 visualization 7 transcriptomics 7 bioconductor-package 7 Cheminformatics 7 single-cell 7 SNP 7 genomics 6 Pharmacogenetics 6 Pharmacogenomics 6 FunctionalPrediction 6 NetworkInference 6 aCGH 6 MultipleSequenceAlignment 6 GenePrediction 5 r-package 5 data-visualization 5 ATACSeq 5 HiC 5 Phylogenetics 5 Survival 5