Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "BiomedicalInformatics" keyword
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 6 months ago - 28.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry3 versions - Latest release: 6 months ago - 9.23 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis3 versions - Latest release: 6 months ago - 1 dependent package - 10.3 thousand downloads total - 1 maintainer
OMICsPCA 1.20.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...3 versions - Latest release: 6 months ago - 7.29 thousand downloads total - 1 maintainer
easier 1.8.0
Estimate Systems Immune Response from RNA-seq data3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting3 versions - Latest release: 6 months ago - 4.72 thousand downloads total - 1 maintainer
powerTCR 1.22.0
Model-Based Comparative Analysis of the TCR Repertoire3 versions - Latest release: 6 months ago - 1 dependent package - 26.9 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
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
ZygosityPredictor 1.2.0
Package for prediction of zygosity for variants/genes in NGS data3 versions - Latest release: 6 months ago - 1.25 thousand downloads total - 1 maintainer
cbaf 1.24.0
Automated functions for comparing various omic data from cbioportal.org3 versions - Latest release: 6 months ago - 8.7 thousand downloads total - 1 maintainer
hummingbird 1.12.0
Bayesian Hidden Markov Model for the detection of differentially methylated regions3 versions - Latest release: 6 months ago - 3.39 thousand downloads total - 1 maintainer
netDx 1.14.0
Network-based patient classifier3 versions - Latest release: 6 months ago - 4.36 thousand downloads total - 1 maintainer
GAprediction 1.28.0
Prediction of gestational age with Illumina HumanMethylation450 data3 versions - Latest release: 6 months ago - 9.4 thousand downloads total - 1 maintainer
miRspongeR 2.6.0
Identification and analysis of miRNA sponge regulation3 versions - Latest release: 6 months ago - 1 dependent package - 6.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
ASAFE 1.28.0
Ancestry Specific Allele Frequency Estimation3 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
coRdon 1.20.0
Codon Usage Analysis and Prediction of Gene Expressivity3 versions - Latest release: 6 months ago - 13 thousand downloads total - 17 stars on GitHub - 1 maintainer
Pigengene 1.28.0
Infers biological signatures from gene expression data3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
frenchFISH 1.14.0
Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections3 versions - Latest release: 6 months ago - 3.9 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: 6 months ago - 7.46 thousand downloads total - 1 maintainer
messina 1.38.0
Single-gene classifiers and outlier-resistant detection of differential expression for two-group ...3 versions - Latest release: 6 months ago - 15.3 thousand downloads total - 1 maintainer
GRaNIE 1.6.1
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...3 versions - Latest release: 6 months ago - 3.75 thousand downloads total - 1 maintainer
psygenet2r 1.34.1
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric...4 versions - Latest release: 4 months ago - 11.5 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
3 versions - Latest release: 6 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: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
RImmPort 1.30.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data3 versions - Latest release: 6 months ago - 9.87 thousand downloads total - 2 maintainers
decompTumor2Sig 2.18.0
Decomposition of individual tumors into mutational signatures by signature refitting3 versions - Latest release: 6 months ago - 1 dependent package - 8.89 thousand downloads total - 1 maintainer
CancerInSilico 2.22.0
An R interface for computational modeling of tumor progression3 versions - Latest release: 6 months ago - 8.93 thousand downloads total - 2 maintainers
rmelting 1.18.0
R Interface to MELTING 53 versions - Latest release: 6 months ago - 6.43 thousand downloads total - 2 stars on GitHub - 1 maintainer
TRONCO 2.34.0
TRONCO, an R package for TRanslational ONCOlogy3 versions - Latest release: 6 months ago - 16.6 thousand downloads total - 1 maintainer
immunotation 1.10.0
Tools for working with diverse immune genes3 versions - Latest release: 6 months ago - 3.1 thousand downloads total - 8 stars on GitHub - 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: 6 months ago - 15.2 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 51.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
fmcsR 1.44.0
Mismatch Tolerant Maximum Common Substructure Searching3 versions - Latest release: 6 months ago - 1 dependent package - 51.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
pfamAnalyzeR 1.2.0
Identification of domain isotypes in pfam data3 versions - Latest release: 6 months ago - 1 dependent package - 4.36 thousand downloads total - 1 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
gCrisprTools 2.8.0
Suite of Functions for Pooled Crispr Screen QC and Analysis3 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 1 maintainer
timescape 1.26.0
Patient Clonal Timescapes3 versions - Latest release: 6 months ago - 11 thousand downloads total - 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: 6 months ago - 5.12 thousand downloads total - 1 maintainer
geneClassifiers 1.26.0
Application of gene classifiers3 versions - Latest release: 6 months ago - 8.67 thousand downloads total - 1 maintainer
dearseq 1.14.0
Differential Expression Analysis for RNA-seq data through a robust variance component test3 versions - Latest release: 6 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: 6 months ago - 5.21 thousand downloads total - 1 maintainer
microSTASIS 1.2.0
Microbiota STability ASsessment via Iterative cluStering3 versions - Latest release: 6 months ago - 1.44 thousand downloads total - 1 maintainer
randRotation 1.14.0
Random Rotation Methods for High Dimensional Data with Batch Structure3 versions - Latest release: 6 months ago - 3.92 thousand downloads total - 0 stars on GitHub - 1 maintainer
ssPATHS 1.16.0
ssPATHS: Single Sample PATHway Score3 versions - Latest release: 6 months ago - 4.47 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.10.0
PhenoGeneRanker: A gene and phenotype prioritization tool3 versions - Latest release: 6 months ago - 2.65 thousand downloads total - 1 maintainer
STROMA4 1.26.0
Assign Properties to TNBC Patients3 versions - Latest release: 6 months ago - 7.9 thousand downloads total - 1 maintainer
SiPSiC 1.2.2
Calculate Pathway Scores for Each Cell in scRNA-Seq Data5 versions - Latest release: 3 months ago - 1.28 thousand downloads total - 1 maintainer
signifinder 1.4.0
Collection and implementation of public transcriptional cancer signatures3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 5 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: 9 days ago - 2.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
mistyR 1.12.0
Multiview Intercellular SpaTial modeling framework4 versions - Latest release: 7 days ago - 4.1 thousand downloads total - 39 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 19 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
IgGeneUsage 1.18.0
Differential gene usage in immune repertoires3 versions - Latest release: 8 days ago - 4.83 thousand downloads total - 6 stars on GitHub - 1 maintainer
fobitools 1.12.0
Tools for Manipulating the FOBI Ontology3 versions - Latest release: 16 days ago - 2.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: 12 days ago - 1 dependent package - 52.1 thousand downloads total - 1 maintainer
flowAI 1.34.0
Automatic and interactive quality control for flow cytometry data3 versions - Latest release: 12 days ago - 1 dependent package - 52.1 thousand downloads total - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network2 versions - Latest release: 13 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
SparseSignatures 2.14.0
SparseSignatures3 versions - Latest release: 15 days ago - 7.65 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 2 dependent packages - 217 thousand downloads total - 9 stars on GitHub - 1 maintainer
ChemmineOB 1.42.0
R interface to a subset of OpenBabel functionalities3 versions - Latest release: 13 days ago - 2 dependent packages - 217 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
DiffBind 3.14.0
Differential Binding Analysis of ChIP-Seq Peak Data3 versions - Latest release: 13 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
miRSM 2.0.0
Inferring miRNA sponge modules in heterogeneous data3 versions - Latest release: 14 days ago - 5.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
RESOLVE 1.6.0
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes3 versions - Latest release: 16 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
psichomics 1.30.0
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation4 versions - Latest release: 15 days ago - 14.4 thousand downloads total - 33 stars on GitHub - 1 maintainer
VERSO 1.14.0
Viral Evolution ReconStructiOn (VERSO)3 versions - Latest release: 15 days ago - 3.43 thousand downloads total - 6 stars on GitHub - 1 maintainer
OncoScore 1.32.0
A tool to identify potentially oncogenic genes3 versions - Latest release: 16 days ago - 11 thousand downloads total - 5 stars on GitHub - 1 maintainer
LACE 2.8.0
Longitudinal Analysis of Cancer Evolution (LACE)4 versions - Latest release: 16 days ago - 4.91 thousand downloads total - 13 stars on GitHub - 1 maintainer
proteasy 1.6.0
Protease Mapping3 versions - Latest release: 18 days ago - 1.07 thousand downloads total - 2 stars on GitHub - 1 maintainer
eiR 1.44.0
Accelerated similarity searching of small molecules3 versions - Latest release: 20 days ago - 15.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
SPIAT 1.6.0
Spatial Image Analysis of Tissues5 versions - Latest release: 20 days ago - 2.95 thousand downloads total - 16 stars on GitHub - 1 maintainer
spaSim 1.6.0
Spatial point data simulator for tissue images3 versions - Latest release: 20 days ago - 1.61 thousand downloads total - 1 stars on GitHub - 1 maintainer
EWCE 1.12.0
Expression Weighted Celltype Enrichment4 versions - Latest release: 20 days ago - 8.86 thousand downloads total - 51 stars on GitHub - 1 maintainer
betaHMM 1.0.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...1 version - Latest release: 21 days ago - 175 downloads total - 1 maintainer
faers 1.0.0
R interface for FDA Adverse Event Reporting System1 version - Latest release: 21 days ago - 171 downloads total - 1 maintainer
ISAnalytics 1.14.0
Analyze gene therapy vector insertion sites data identified from genomics next generation sequenc...3 versions - Latest release: 21 days ago - 3.63 thousand downloads total - 3 stars on GitHub - 1 maintainer
RIVER 1.26.0
R package for RIVER (RNA-Informed Variant Effect on Regulation)2 versions - Latest release: 6 months ago - 8.53 thousand downloads total - 10 stars on GitHub - 1 maintainer
cfTools 1.2.0
Informatics Tools for Cell-Free DNA Study2 versions - Latest release: 6 months ago - 946 downloads total - 5 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
2 versions - Latest release: 6 months ago - 8 dependent packages - 481 thousand downloads total - 13 stars on GitHub - 1 maintainer
ChemmineR 3.54.0
Cheminformatics Toolkit for R2 versions - Latest release: 6 months ago - 8 dependent packages - 481 thousand downloads total - 13 stars on GitHub - 1 maintainer
MEAT 1.14.0
Muscle Epigenetic Age Test2 versions - Latest release: 6 months ago - 4.16 thousand downloads total - 0 stars on GitHub - 1 maintainer
MOGAMUN 1.12.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks2 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 12 stars on GitHub - 1 maintainer
OPWeight 1.24.0
Optimal p-value weighting with independent information2 versions - Latest release: 6 months ago - 16.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
protGear 1.6.0
Protein Micro Array Data Management and Interactive Visualization2 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 stars on GitHub - 1 maintainer
simona 1.0.10
Semantic Similarity in Bio-Ontologies3 versions - Latest release: 3 months ago - 964 downloads total - 7 stars on GitHub - 1 maintainer
gwasurvivr 1.20.0
gwasurvivr: an R package for genome wide survival analysis2 versions - Latest release: 6 months ago - 9.23 thousand downloads total - 9 stars on GitHub - 1 maintainer
SigsPack 1.16.0
Mutational Signature Estimation for Single Samples2 versions - Latest release: 6 months ago - 4.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
drugTargetInteractions 1.10.1
Drug-Target Interactions2 versions - Latest release: 6 months ago - 3.03 thousand downloads total - 1 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks2 versions - Latest release: 6 months ago - 1 dependent package - 9.31 thousand downloads total - 17 stars on GitHub - 1 maintainer
oppti 1.16.0
Outlier Protein and Phosphosite Target Identifier2 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 2 stars on GitHub - 1 maintainer
MouseFM 1.12.0
In-silico methods for genetic finemapping in inbred mice2 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients1 version - Latest release: 7 months ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
88
GeneExpression
30
SystemsBiology
28
ImmunoOncology
27
Clustering
26
RNASeq
24
Transcriptomics
21
DifferentialExpression
20
DataImport
19
Sequencing
19
Genetics
19
Regression
17
Transcription
17
FunctionalGenomics
17
MultipleComparison
16
Microarray
16
Visualization
16
GeneSetEnrichment
16
Proteomics
15
CellBiology
14
SingleCell
12
Epigenetics
12
Normalization
12
Network
11
GraphAndNetwork
11
SomaticMutation
10
Cheminformatics
10
Pathways
10
Classification
10
Bayesian
10
QualityControl
9
Metabolomics
9
Pharmacogenomics
8
DNAMethylation
8
Preprocessing
8
AlternativeSplicing
8
GenePrediction
8
Annotation
7
Survival
7
Infrastructure
7
SNP
7
BatchEffect
7
Spatial
6
DifferentialSplicing
6
DifferentialMethylation
6
Pharmacogenetics
6
DataRepresentation
6
NetworkInference
6
GeneRegulation
5
KEGG
5
GeneTarget
5
TimeCourse
5
GenomicVariation
5
MathematicalBiology
5
StatisticalMethod
5
DimensionReduction
5
ChIPSeq
5
FunctionalPrediction
5
r
5
mRNAMicroarray
5
GeneticVariability
5
CellBasedAssays
4
OneChannel
4
MicrotitrePlateAssay
4
FeatureExtraction
4
MicroRNAArray
4
PrincipalComponent
4
bioinformatics
3
bioconductor
3
DNASeq
3
Coverage
3
ExonArray
3
ReportWriting
3
ProprietaryPlatforms
3
ExperimentalDesign
3
BiologicalQuestion
3
GO
3
HiddenMarkovModel
3
TranscriptomeVariant
3
ATACSeq
3
WorkflowStep
2
GUI
2
VariantAnnotation
2
DecisionTree
2
transcriptomics
2
MassSpectrometry
2
MethylationArray
2
PatternLogic
2
GenomeWideAssociation
2
TwoChannel
2
mirna
2
cerna
2
MethylSeq
2
differential-gene-expression
2
r-package
2
NetworkEnrichment
2
bayesian
1
functionalgenomics
1
biomedicalinformatics
1
single-cell-rna-seq
1