Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "StatisticalMethod" keyword
RGSEA 1.36.0
Random Gene Set Enrichment Analysis3 versions - Latest release: 6 months ago - 17.3 thousand downloads total - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data3 versions - Latest release: 6 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
CyTOFpower 1.8.0
Power analysis for CyTOF experiments3 versions - Latest release: 6 months ago - 2.32 thousand downloads total - 1 maintainer
bacon 1.30.0
Controlling bias and inflation in association studies using the empirical null distribution3 versions - Latest release: 6 months ago - 16.9 thousand downloads total - 1 maintainer
npGSEA 1.38.0
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)3 versions - Latest release: 6 months ago - 17.7 thousand downloads total - 1 maintainer
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles3 versions - Latest release: 6 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
cpvSNP 1.34.0
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets3 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 1 maintainer
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
stageR 1.24.0
stageR: stage-wise analysis of high throughput gene expression data in R3 versions - Latest release: 6 months ago - 2 dependent packages - 18.4 thousand downloads total - 1 maintainer
FunChIP 1.28.0
Clustering and Alignment of ChIP-Seq peaks based on their shapes3 versions - Latest release: 6 months ago - 9.68 thousand downloads total - 1 maintainer
switchBox 1.38.0
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair ...3 versions - Latest release: 6 months ago - 1 dependent package - 18.3 thousand downloads total - 3 maintainers
midasHLA 1.10.0
R package for immunogenomics data handling and association analysis3 versions - Latest release: 6 months ago - 5.76 thousand downloads total - 1 maintainer
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...3 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
TitanCNA 1.40.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours3 versions - Latest release: 6 months ago - 22.4 thousand downloads total - 87 stars on GitHub - 1 maintainer
dcGSA 1.30.0
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles3 versions - Latest release: 6 months ago - 10.5 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
randPack 1.48.0
Randomization routines for Clinical Trials3 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 1 maintainer
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects3 versions - Latest release: 6 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
Mulcom 1.52.0
Calculates Mulcom test3 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
DeMixT 1.18.0
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components usin...3 versions - Latest release: 6 months ago - 7.82 thousand downloads total - 1 maintainer
padma 1.12.0
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis3 versions - Latest release: 6 months ago - 3.61 thousand downloads total - 3 stars on GitHub - 1 maintainer
HiLDA 1.16.0
Conducting statistical inference on comparing the mutational exposures of mutational signatures b...3 versions - Latest release: 6 months ago - 1 dependent package - 5.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
target 1.16.0
Predict Combined Function of Transcription Factors3 versions - Latest release: 6 months ago - 4.73 thousand downloads total - 4 stars on GitHub - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data3 versions - Latest release: 6 months ago - 1.98 thousand downloads total - 1 maintainer
STATegRa 1.38.0
Classes and methods for multi-omics data integration3 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 2 maintainers
PING 2.46.0
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 1 maintainer
GPA 1.14.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)3 versions - Latest release: 6 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
receptLoss 1.14.0
Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors3 versions - Latest release: 6 months ago - 3.75 thousand downloads total - 1 maintainer
methylInheritance 1.26.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
pareg 1.6.0
Pathway enrichment using a regularized regression approach3 versions - Latest release: 6 months ago - 1.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
treekoR 1.10.0
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations3 versions - Latest release: 6 months ago - 2.99 thousand downloads total - 1 maintainer
PAIRADISE 1.18.0
PAIRADISE: Paired analysis of differential isoform expression3 versions - Latest release: 6 months ago - 7.24 thousand downloads total - 2 maintainers
AWFisher 1.16.0
An R package for fast computing for adaptively weighted fisher's method3 versions - Latest release: 6 months ago - 6.03 thousand downloads total - 3 stars on GitHub - 1 maintainer
IWTomics 1.26.0
Interval-Wise Testing for Omics Data3 versions - Latest release: 6 months ago - 9.28 thousand downloads total - 1 maintainer
FeatSeekR 1.2.0
FeatSeekR an R package for unsupervised feature selection3 versions - Latest release: 6 months ago - 1.19 thousand downloads total - 1 stars on GitHub - 1 maintainer
Summix 2.8.0
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data3 versions - Latest release: 6 months ago - 2.59 thousand downloads total - 1 maintainer
mosbi 1.8.0
Molecular Signature identification using Biclustering3 versions - Latest release: 6 months ago - 2.63 thousand downloads total - 1 maintainer
RJMCMCNucleosomes 1.26.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...3 versions - Latest release: 6 months ago - 9.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
Rtreemix 1.64.0
Rtreemix: Mutagenetic trees mixture models.3 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
CTSV 1.4.0
Identification of cell-type-specific spatially variable genes accounting for excess zeros3 versions - Latest release: 6 months ago - 1.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
tweeDEseq 1.48.0
RNA-seq data analysis using the Poisson-Tweedie family of distributions3 versions - Latest release: 6 months ago - 32.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
ASSET 2.20.0
An R package for subset-based association analysis of heterogeneous traits and subtypes3 versions - Latest release: 6 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
NeighborNet 1.20.0
Neighbor_net analysis3 versions - Latest release: 6 months ago - 4.32 thousand downloads total - 1 maintainer
synergyfinder 3.10.3
Calculate and Visualize Synergy Scores for Drug Combinations4 versions - Latest release: 3 months ago - 23.5 thousand downloads total - 1 maintainer
Harman 1.30.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique3 versions - Latest release: 6 months ago - 1 dependent package - 20.4 thousand downloads total - 1 maintainer
GSAR 1.36.0
Gene Set Analysis in R3 versions - Latest release: 6 months ago - 23.1 thousand downloads total - 2 maintainers
CytoDx 1.22.0
Robust prediction of clinical outcomes using cytometry data without cell gating3 versions - Latest release: 6 months ago - 7.94 thousand downloads total - 1 maintainer
phosphonormalizer 1.26.0
Compensates for the bias introduced by median normalization in3 versions - Latest release: 6 months ago - 9.22 thousand downloads total - 1 maintainer
INDEED 2.16.0
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis...3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 4 stars on GitHub - 2 maintainers
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
dStruct 1.8.0
Identifying differentially reactive regions from RNA structurome profiling data3 versions - Latest release: 6 months ago - 2.33 thousand downloads total - 2 stars on GitHub - 1 maintainer
iCARE 1.30.0
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)3 versions - Latest release: 6 months ago - 13.9 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 27.5 thousand downloads total - 1 maintainer
MeasurementError.cor 1.74.0
Measurement Error model estimate for correlation coefficient3 versions - Latest release: 6 months ago - 27.5 thousand downloads total - 1 maintainer
profileScoreDist 1.30.0
Profile score distributions3 versions - Latest release: 6 months ago - 9.22 thousand downloads total - 1 maintainer
MethylMix 2.32.0
MethylMix: Identifying methylation driven cancer genes3 versions - Latest release: 6 months ago - 22.2 thousand downloads total - 1 maintainer
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
rSWeeP 1.14.0
Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences3 versions - Latest release: 6 months ago - 4.28 thousand downloads total - 1 maintainer
ORFhunteR 1.10.0
Predict open reading frames in nucleotide sequences3 versions - Latest release: 6 months ago - 3.05 thousand downloads total - 1 stars on GitHub - 1 maintainer
srnadiff 1.22.2
Finding differentially expressed unannotated genomic regions from RNA-seq data4 versions - Latest release: 2 months ago - 7.11 thousand downloads total - 1 maintainer
methInheritSim 1.24.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data3 versions - Latest release: 6 months ago - 1 dependent package - 8.46 thousand downloads total - 1 stars on GitHub - 1 maintainer
deltaCaptureC 1.16.1
This Package Discovers Meso-scale Chromatin Remodeling from 3C Data4 versions - Latest release: about 1 month ago - 4.87 thousand downloads total - 1 maintainer
BiocSklearn 1.24.0
interface to python sklearn via Rstudio reticulate3 versions - Latest release: 6 months ago - 15.9 thousand downloads total - 1 maintainer
VaSP 1.14.0
Quantification and Visualization of Variations of Splicing in Population3 versions - Latest release: 6 months ago - 3.14 thousand downloads total - 3 stars on GitHub - 1 maintainer
TFARM 1.24.0
Transcription Factors Association Rules Miner3 versions - Latest release: 6 months ago - 7.46 thousand downloads total - 1 maintainer
survtype 1.18.0
Subtype Identification with Survival Data3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
MAI 1.8.0
Mechanism-Aware Imputation3 versions - Latest release: 6 months ago - 2.68 thousand downloads total - 1 stars on GitHub - 1 maintainer
DExMA 1.10.7
Differential Expression Meta-Analysis4 versions - Latest release: 5 months ago - 3.5 thousand downloads total - 1 maintainer
MetaCyto 1.24.0
MetaCyto: A package for meta-analysis of cytometry data3 versions - Latest release: 6 months ago - 9.82 thousand downloads total - 1 maintainer
pandaR 1.34.0
PANDA Algorithm3 versions - Latest release: 6 months ago - 1 dependent package - 16.7 thousand downloads total - 2 maintainers
DeMAND 1.32.0
DeMAND3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 2 maintainers
peco 1.14.0
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data3 versions - Latest release: 6 months ago - 4.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
MultiMed 2.24.0
Testing multiple biological mediators simultaneously3 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 1 maintainer
missRows 1.22.0
Handling Missing Individuals in Multi-Omics Data Integration3 versions - Latest release: 6 months ago - 6.95 thousand downloads total - 1 maintainer
MetID 1.20.0
Network-based prioritization of putative metabolite IDs3 versions - Latest release: 6 months ago - 5.66 thousand downloads total - 1 stars on GitHub - 1 maintainer
OpenStats 1.14.0
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phen...3 versions - Latest release: 6 months ago - 4.39 thousand downloads total - 1 maintainer
MCbiclust 1.26.0
Massive correlating biclusters for gene expression data and associated methods3 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
TrajectoryGeometry 1.10.1
This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns4 versions - Latest release: 2 months ago - 2.54 thousand downloads total - 1 maintainer
MultiBaC 1.12.0
Multiomic Batch effect Correction3 versions - Latest release: 6 months ago - 4.52 thousand downloads total - 1 maintainer
ClusterJudge 1.24.0
Judging Quality of Clustering Methods using Mutual Information3 versions - Latest release: 6 months ago - 7.83 thousand downloads total - 1 maintainer
garfield 1.30.0
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 1 maintainer
omicRexposome 1.24.3
Exposome and omic data associatin and integration analysis4 versions - Latest release: 3 months ago - 7.99 thousand downloads total - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 6 months ago - 1.26 thousand downloads total - 1 maintainer
YAPSA 1.28.0
Yet Another Package for Signature Analysis3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 1 maintainer
discordant 1.26.0
The Discordant Method: A Novel Approach for Differential Correlation3 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 10 stars on GitHub - 1 maintainer
beer 1.6.0
Bayesian Enrichment Estimation in R3 versions - Latest release: 6 months ago - 2.33 thousand downloads total - 5 stars on GitHub - 1 maintainer
waddR 1.16.0
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance3 versions - Latest release: 6 months ago - 5.85 thousand downloads total - 24 stars on GitHub - 1 maintainer
PhenStat 2.38.0
Statistical analysis of phenotypic data3 versions - Latest release: 6 months ago - 17.1 thousand downloads total - 1 maintainer
divergence 1.18.0
Divergence: Functionality for assessing omics data by divergence with respect to a baseline3 versions - Latest release: 6 months ago - 5.14 thousand downloads total - 2 maintainers
selectKSigs 1.14.0
Selecting the number of mutational signatures using a perplexity-based measure and cross-validation3 versions - Latest release: 6 months ago - 4.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
RUVnormalize 1.36.0
RUV for normalization of expression array data3 versions - Latest release: 6 months ago - 16.3 thousand downloads total - 1 maintainer
gsean 1.22.0
Gene Set Enrichment Analysis with Networks3 versions - Latest release: 6 months ago - 7.81 thousand downloads total - 1 maintainer
metaCCA 1.30.0
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Cano...3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 maintainer
PPInfer 1.28.0
Inferring functionally related proteins using protein interaction networks3 versions - Latest release: 6 months ago - 1 dependent package - 11.3 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
Uniquorn 2.22.0
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint3 versions - Latest release: 6 months ago - 10.2 thousand downloads total - 1 maintainer
BUScorrect 1.20.0
Batch Effects Correction with Unknown Subtypes3 versions - Latest release: 6 months ago - 6.23 thousand downloads total - 1 maintainer
iasva 1.20.0
Iteratively Adjusted Surrogate Variable Analysis3 versions - Latest release: 6 months ago - 6.5 thousand downloads total - 2 maintainers
granulator 1.10.0
Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data3 versions - Latest release: 6 months ago - 1 dependent package - 6.04 thousand downloads total - 1 stars on GitHub - 1 maintainer
EBSeqHMM 1.35.0
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
CIMICE 1.10.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution3 versions - Latest release: 6 months ago - 3.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software
169
GeneExpression
55
DifferentialExpression
43
Sequencing
43
ImmunoOncology
36
RNASeq
32
Clustering
30
Visualization
25
Genetics
23
MultipleComparison
23
SingleCell
20
Regression
20
Preprocessing
19
Classification
19
Microarray
18
Network
17
BatchEffect
15
Bayesian
15
BiologicalQuestion
14
PrincipalComponent
14
Transcriptomics
13
Transcription
13
Normalization
12
GraphAndNetwork
11
DimensionReduction
11
FlowCytometry
11
GeneSetEnrichment
10
GenomeWideAssociation
10
DNAMethylation
9
Pathways
9
r
9
SNP
7
FeatureExtraction
7
Coverage
7
CellBiology
7
MassSpectrometry
7
Proteomics
7
bioconductor
7
CellBasedAssays
7
AlternativeSplicing
7
GenomicVariation
7
DifferentialMethylation
7
NetworkEnrichment
6
GeneRegulation
6
WholeGenome
6
Metabolomics
6
SomaticMutation
6
DifferentialSplicing
6
DataImport
6
QualityControl
6
bioinformatics
6
Technology
6
TimeCourse
5
Epigenetics
5
Spatial
5
bioconductor-package
5
BiomedicalInformatics
5
ResearchField
4
Survival
4
MethylationArray
4
KEGG
4
GeneTarget
4
DNASeq
4
Infrastructure
4
ExperimentalDesign
4
r-package
4
SystemsBiology
4
Annotation
3
WorkflowStep
3
Microbiome
3
HiddenMarkovModel
3
CopyNumberVariation
3
MethylSeq
3
NetworkInference
3
Alignment
2
SupportVectorMachine
2
rstats
2
snp
2
nucleosomes
2
methylation
2
GenomeAnnotation
2
simulation
2
ExomeSeq
2
inheritance
2
GO
2
dna-methylation
2
ChIPSeq
2
FunctionalGenomics
2
FunctionalPrediction
2
GenePrediction
2
mRNAMicroarray
2
bioconductor-packages
2
statistics
2
MicroRNAArray
2
machine-learning
2
missing-data
2
MultidimensionalScaling
1
DecisionTree
1
GeneticVariability
1
PooledScreens
1