Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "SystemsBiology" keyword
MIRit 0.99.13
Integrate microRNA and gene expression to decipher pathway complexity2 versions - Latest release: about 1 month ago - 346 downloads total - 0 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
3 versions - Latest release: about 1 month ago - 4 dependent packages - 172 thousand downloads total - 5 stars on GitHub - 1 maintainer
gage 2.54.0
Generally Applicable Gene-set Enrichment for Pathway Analysis3 versions - Latest release: about 1 month ago - 4 dependent packages - 172 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
3 versions - Latest release: about 1 month ago - 9 dependent packages - 509 thousand downloads total - 32 stars on GitHub - 1 maintainer
pathview 1.44.0
a tool set for pathway based data integration and visualization3 versions - Latest release: about 1 month ago - 9 dependent packages - 509 thousand downloads total - 32 stars on GitHub - 1 maintainer
DeProViR 1.0.0
A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Prot...1 version - Latest release: about 1 month ago - 364 downloads total - 1 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)3 versions - Latest release: 7 months ago - 8.83 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: about 1 month ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: about 1 month ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: about 1 month ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis3 versions - Latest release: 7 months ago - 17.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
CCPlotR 1.0.0
Plots For Visualising Cell-Cell Interactions2 versions - Latest release: 7 months ago - 1.09 thousand downloads total - 22 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 116 thousand downloads total - 273 stars on GitHub - 1 maintainer
microbiome 1.24.0
Microbiome Analytics3 versions - Latest release: 6 months ago - 2 dependent packages - 116 thousand downloads total - 273 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis3 versions - Latest release: 6 months ago - 8.68 thousand downloads total - 7 stars on GitHub - 1 maintainer
MOGAMUN 1.12.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks3 versions - Latest release: 6 months ago - 3.79 thousand downloads total - 12 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
protGear 1.6.0
Protein Micro Array Data Management and Interactive Visualization3 versions - Latest release: 7 months ago - 2.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
MOMA 1.14.0
Multi Omic Master Regulator Analysis3 versions - Latest release: 6 months ago - 4.74 thousand downloads total - 5 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
transcriptogramer 1.24.0
Transcriptional analysis based on transcriptograms3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 4 stars on GitHub - 1 maintainer
paxtoolsr 1.36.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons3 versions - Latest release: 6 months ago - 24 thousand downloads total - 10 stars on GitHub - 1 maintainer
MouseFM 1.12.0
In-silico methods for genetic finemapping in inbred mice3 versions - Latest release: 6 months ago - 5.37 thousand downloads total - 0 stars on GitHub - 1 maintainer
BioCor 1.26.0
Functional similarities3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
diggit 1.34.0
Inference of Genetic Variants Driving Cellular Phenotypes3 versions - Latest release: 7 months ago - 13.4 thousand downloads total - 1 maintainer
MIRA 1.24.0
Methylation-Based Inference of Regulatory Activity3 versions - Latest release: 7 months ago - 1 dependent package - 10.5 thousand downloads total - 1 maintainer
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 7 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
epidecodeR 1.10.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 7 months ago - 28.3 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 7 dependent packages - 57.3 thousand downloads total - 1 maintainer
viper 1.36.0
Virtual Inference of Protein-activity by Enriched Regulon analysis3 versions - Latest release: 7 months ago - 7 dependent packages - 57.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry3 versions - Latest release: 7 months ago - 9.23 thousand downloads total - 1 maintainer
SPONGE 1.24.0
Sparse Partial Correlations On Gene Expression3 versions - Latest release: 7 months ago - 2 dependent packages - 8.57 thousand downloads total - 1 maintainer
MEIGOR 1.36.2
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization5 versions - Latest release: about 1 month ago - 2 dependent packages - 16.9 thousand downloads total - 1 maintainer
syntenet 1.4.2
Inference And Analysis Of Synteny Networks4 versions - Latest release: about 1 month ago - 1 dependent package - 3.4 thousand downloads total - 14 stars on GitHub - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 7 months ago - 4.36 thousand downloads total - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
geva 1.10.0
Gene Expression Variation Analysis (GEVA)3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
Path2PPI 1.32.0
Prediction of pathway-related protein-protein interaction networks3 versions - Latest release: 7 months ago - 12.6 thousand downloads total - 1 maintainer
GmicR 1.16.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...3 versions - Latest release: 7 months ago - 5.69 thousand downloads total - 1 maintainer
sRACIPE 1.18.0
Systems biology tool to simulate gene regulatory circuits3 versions - Latest release: 7 months ago - 5.77 thousand downloads total - 0 stars on GitHub - 1 maintainer
KBoost 1.10.0
Inference of gene regulatory networks from gene expression data3 versions - Latest release: 7 months ago - 2.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
pmm 1.34.0
Parallel Mixed Model3 versions - Latest release: 7 months ago - 11.2 thousand downloads total - 1 maintainer
PrInCE 1.18.0
Predicting Interactomes from Co-Elution3 versions - Latest release: 7 months ago - 5.92 thousand downloads total - 6 stars on GitHub - 1 maintainer
IMMAN 1.22.0
Interlog protein network reconstruction by Mapping and Mining ANalysis3 versions - Latest release: 7 months ago - 7.17 thousand downloads total - 1 maintainer
netDx 1.14.0
Network-based patient classifier3 versions - Latest release: 7 months ago - 4.36 thousand downloads total - 1 maintainer
Top 6.4% on bioconductor.org
3 versions - Latest release: 7 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
hpar 1.44.0
Human Protein Atlas in R3 versions - Latest release: 7 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges3 versions - Latest release: 7 months ago - 5 dependent packages - 25 thousand downloads total - 1 maintainer
MWASTools 1.26.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies3 versions - Latest release: 7 months ago - 1 dependent package - 13.6 thousand downloads total - 2 maintainers
rcellminer 2.24.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines3 versions - Latest release: 7 months ago - 15.7 thousand downloads total - 3 maintainers
EGAD 1.30.0
Extending guilt by association by degree3 versions - Latest release: 7 months ago - 13.4 thousand downloads total - 1 maintainer
DEsubs 1.28.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...3 versions - Latest release: 7 months ago - 11.1 thousand downloads total - 2 maintainers
Pigengene 1.28.0
Infers biological signatures from gene expression data3 versions - Latest release: 7 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
mdp 1.22.0
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their ...3 versions - Latest release: 7 months ago - 7.46 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
Rcpi 1.38.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery3 versions - Latest release: 7 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
KnowSeq 1.16.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline3 versions - Latest release: 7 months ago - 6.15 thousand downloads total - 1 maintainer
CancerInSilico 2.22.0
An R interface for computational modeling of tumor progression3 versions - Latest release: 7 months ago - 8.93 thousand downloads total - 2 maintainers
CausalR 1.34.0
Causal network analysis methods3 versions - Latest release: 7 months ago - 13.2 thousand downloads total - 2 maintainers
CoRegNet 1.40.0
CoRegNet : reconstruction and integrated analysis of co-regulatory networks3 versions - Latest release: 7 months ago - 16.9 thousand downloads total - 1 maintainer
DeMAND 1.32.0
DeMAND3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 2 maintainers
XINA 1.20.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis3 versions - Latest release: 7 months ago - 6.4 thousand downloads total - 1 maintainer
sincell 1.34.0
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data3 versions - Latest release: 7 months ago - 15.2 thousand downloads total - 1 maintainer
oppar 1.30.0
Outlier profile and pathway analysis in R3 versions - Latest release: 7 months ago - 10.1 thousand downloads total - 1 maintainer
SMITE 1.30.0
Significance-based Modules Integrating the Transcriptome and Epigenome3 versions - Latest release: 7 months ago - 11.9 thousand downloads total - 1 stars on GitHub - 2 maintainers
INSPEcT 1.32.1
Modeling RNA synthesis, processing and degradation with RNA-seq data4 versions - Latest release: 5 months ago - 14.3 thousand downloads total - 2 maintainers
Top 9.8% on bioconductor.org
4 versions - Latest release: 5 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 5 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
pfamAnalyzeR 1.2.0
Identification of domain isotypes in pfam data3 versions - Latest release: 7 months ago - 1 dependent package - 4.36 thousand downloads total - 1 stars on GitHub - 1 maintainer
gCrisprTools 2.8.0
Suite of Functions for Pooled Crispr Screen QC and Analysis3 versions - Latest release: 7 months ago - 11.6 thousand downloads total - 1 maintainer
genomicInstability 1.8.0
Genomic Instability estimation for scRNA-Seq3 versions - Latest release: 7 months ago - 2.32 thousand downloads total - 4 stars on GitHub - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 7 months ago - 5.12 thousand downloads total - 1 maintainer
doseR 1.18.0
doseR3 versions - Latest release: 7 months ago - 5.54 thousand downloads total - 1 maintainer
wppi 1.10.0
Weighting protein-protein interactions3 versions - Latest release: 7 months ago - 3.14 thousand downloads total - 2 stars on GitHub - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 7 months ago - 1.05 thousand downloads total - 0 stars on GitHub - 1 maintainer
dearseq 1.14.0
Differential Expression Analysis for RNA-seq data through a robust variance component test3 versions - Latest release: 7 months ago - 2 dependent packages - 8.25 thousand downloads total - 6 stars on GitHub - 1 maintainer
GenomicOZone 1.16.0
Delineate outstanding genomic zones of differential gene activity3 versions - Latest release: 7 months ago - 5.21 thousand downloads total - 1 maintainer
geneplast 1.28.0
Evolutionary and plasticity analysis of orthologous groups3 versions - Latest release: 7 months ago - 1 dependent package - 10.8 thousand downloads total - 1 maintainer
CHRONOS 1.30.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis3 versions - Latest release: 7 months ago - 12 thousand downloads total - 1 maintainer
multiOmicsViz 1.26.0
Plot the effect of one omics data on other omics data along the chromosome3 versions - Latest release: 7 months ago - 9.01 thousand downloads total - 1 maintainer
rain 1.36.0
Rhythmicity Analysis Incorporating Non-parametric Methods3 versions - Latest release: 7 months ago - 19.2 thousand downloads total - 1 maintainer
GenomicSuperSignature 1.10.0
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases3 versions - Latest release: 7 months ago - 3.29 thousand downloads total - 12 stars on GitHub - 1 maintainer
vulcan 1.24.0
VirtUaL ChIP-Seq data Analysis using Networks3 versions - Latest release: 7 months ago - 8.7 thousand downloads total - 1 maintainer
HPiP 1.8.0
Host-Pathogen Interaction Prediction3 versions - Latest release: 7 months ago - 2.55 thousand downloads total - 3 stars on GitHub - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 7 months ago - 7.09 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.10.0
PhenoGeneRanker: A gene and phenotype prioritization tool3 versions - Latest release: 7 months ago - 2.65 thousand downloads total - 1 maintainer
pwOmics 1.34.0
Pathway-based data integration of omics data3 versions - Latest release: 7 months ago - 13.6 thousand downloads total - 1 maintainer
trena 1.24.0 removed
Fit transcriptional regulatory networks using gene expression, priors, machine learning2 versions - Latest release: 7 months ago - 7 thousand downloads total - 1 stars on GitHub - 1 maintainer
cytoMEM 1.6.0
Marker Enrichment Modeling (MEM)3 versions - Latest release: 7 months ago - 2.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
rsemmed 1.12.0
An interface to the Semantic MEDLINE database3 versions - Latest release: 7 months ago - 3.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
sitadela 1.12.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...3 versions - Latest release: 20 days ago - 2.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
progeny 1.26.0
Pathway RespOnsive GENes for activity inference from gene expression3 versions - Latest release: 19 days ago - 2 dependent packages - 26.5 thousand downloads total - 88 stars on GitHub - 1 maintainer
mistyR 1.12.0
Multiview Intercellular SpaTial modeling framework4 versions - Latest release: 19 days ago - 4.1 thousand downloads total - 39 stars on GitHub - 1 maintainer
COTAN 2.4.1
COexpression Tables ANalysis6 versions - Latest release: 19 days ago - 3.11 thousand downloads total - 14 stars on GitHub - 1 maintainer
SBGNview 1.18.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"3 versions - Latest release: 20 days ago - 7.83 thousand downloads total - 23 stars on GitHub - 1 maintainer
netOmics 1.10.0
Multi-Omics (time-course) network-based integration and interpretation3 versions - Latest release: 20 days ago - 2.23 thousand downloads total - 5 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 24 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 24 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
GENIE3 1.26.0
GEne Network Inference with Ensemble of trees3 versions - Latest release: 24 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
4 versions - Latest release: 24 days ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
RedeR 3.0.0
Interactive visualization and manipulation of nested networks4 versions - Latest release: 24 days ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network2 versions - Latest release: 25 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
3 versions - Latest release: 25 days ago - 4 dependent packages - 106 thousand downloads total - 1 maintainer
RankProd 3.30.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis3 versions - Latest release: 25 days ago - 4 dependent packages - 106 thousand downloads total - 1 maintainer
magrene 1.6.0
Motif Analysis In Gene Regulatory Networks3 versions - Latest release: 25 days ago - 1.45 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus5 versions - Latest release: 25 days ago - 1 dependent package - 8.17 thousand downloads total - 17 stars on GitHub - 1 maintainer
ceRNAnetsim 1.16.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)4 versions - Latest release: 26 days ago - 4.14 thousand downloads total - 4 stars on GitHub - 1 maintainer
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements3 versions - Latest release: 27 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
108
GeneExpression
55
Network
44
GraphAndNetwork
32
Pathways
31
RNASeq
30
Transcriptomics
29
BiomedicalInformatics
28
DifferentialExpression
28
NetworkInference
27
GeneSetEnrichment
25
GeneRegulation
24
FunctionalGenomics
24
Proteomics
24
ImmunoOncology
23
Sequencing
23
Clustering
22
Transcription
19
Microarray
18
Regression
17
Genetics
17
NetworkEnrichment
17
Visualization
15
MultipleComparison
14
CellBiology
14
DataImport
12
Classification
12
KEGG
11
Normalization
11
SingleCell
10
QualityControl
10
FunctionalPrediction
10
Epigenetics
10
GenePrediction
9
Bayesian
9
Metabolomics
9
AlternativeSplicing
8
FeatureExtraction
8
TimeCourse
8
Preprocessing
8
r
8
GeneTarget
7
GeneSignaling
7
Annotation
7
ChIPSeq
7
BatchEffect
7
PrincipalComponent
6
GO
6
MathematicalBiology
6
DNAMethylation
6
GenomicVariation
6
DataRepresentation
5
Cheminformatics
5
Reactome
5
DifferentialSplicing
5
DimensionReduction
5
OneChannel
5
GenomeAnnotation
5
StatisticalMethod
4
SNP
4
Coverage
4
ATACSeq
4
DifferentialMethylation
4
mRNAMicroarray
4
TwoChannel
4
DNASeq
4
bioinformatics
4
CopyNumberVariation
4
ProprietaryPlatforms
3
bioconductor
3
Lipidomics
3
TranscriptomeVariant
3
Survival
3
NeuralNetwork
3
clustering
3
rstats
3
DecisionTree
3
CRISPR
3
MethylSeq
3
PooledScreens
3
WorkflowStep
3
ExperimentHubSoftware
2
GenomeWideAssociation
2
GUI
2
ResearchField
2
biology
2
network-science
2
SomaticMutation
2
ComparativeGenomics
2
Alignment
2
networks
2
PatternLogic
2
Pharmacogenetics
2
genomics
2
Pharmacogenomics
2
gene
2
ExonArray
2
genetics
2
MicroRNAArray
2
GeneticVariability
2