Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Regression" keyword
spillR 0.99.10
Spillover Compensation in Mass Cytometry Data2 versions - Latest release: about 1 month ago - 392 downloads total - 1 maintainer
methyLImp2 1.0.0
Missing value estimation of DNA methylation data1 version - Latest release: about 1 month ago - 356 downloads total - 4 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes2 versions - Latest release: about 1 month ago - 292 downloads total - 0 stars on GitHub - 1 maintainer
saseR 1.0.0
Scalable Aberrant Splicing and Expression Retrieval1 version - Latest release: about 1 month ago - 369 downloads total - 1 stars on GitHub - 1 maintainer
findIPs 1.0.0
Influential Points Detection for Feature Rankings1 version - Latest release: about 1 month ago - 188 downloads total - 0 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
proDA 1.16.0
Differential Abundance Analysis of Label-Free Mass Spectrometry Data3 versions - Latest release: 7 months ago - 1 dependent package - 11.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 30 days 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: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
multiWGCNA 1.0.0
multiWGCNA2 versions - Latest release: 7 months ago - 1.32 thousand downloads total - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression6 versions - Latest release: 5 months ago - 1.29 thousand downloads total - 73 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
6 versions - Latest release: 18 days ago - 5 dependent packages - 149 thousand downloads total - 92 stars on GitHub - 1 maintainer
glmGamPoi 1.16.0
Fit a Gamma-Poisson Generalized Linear Model6 versions - Latest release: 18 days ago - 5 dependent packages - 149 thousand downloads total - 92 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...3 versions - Latest release: 27 days ago - 1.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
demuxmix 1.4.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models3 versions - Latest release: 7 months ago - 1 dependent package - 4.55 thousand downloads total - 4 stars on GitHub - 1 maintainer
RolDE 1.6.0
RolDE: Robust longitudinal Differential Expression3 versions - Latest release: 7 months ago - 1.97 thousand downloads total - 4 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
roastgsa 1.0.0
Rotation based gene set analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
SOMNiBUS 1.10.0
Smooth modeling of bisulfite sequencing3 versions - Latest release: 6 months ago - 3.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
Trendy 1.24.1
Breakpoint analysis of time-course expression data4 versions - Latest release: 6 months ago - 8.57 thousand downloads total - 6 stars on GitHub - 1 maintainer
OPWeight 1.24.0
Optimal p-value weighting with independent information3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
CytoGLMM 1.10.0
Conditional Differential Analysis for Flow and Mass Cytometry Experiments3 versions - Latest release: 6 months ago - 1 dependent package - 3.99 thousand downloads total - 2 stars on GitHub - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing3 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 0 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
Top 0.5% on bioconductor.org
4 versions - Latest release: about 1 month ago - 146 dependent packages - 2.78 million downloads total - 330 stars on GitHub - 1 maintainer
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution4 versions - Latest release: about 1 month ago - 146 dependent packages - 2.78 million downloads total - 330 stars on GitHub - 1 maintainer
DMCFB 1.16.1
Differentially Methylated Cytosines via a Bayesian Functional Approach4 versions - Latest release: 3 months ago - 4.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
sevenC 1.22.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs3 versions - Latest release: 6 months ago - 7.5 thousand downloads total - 12 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
methylSig 1.14.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data3 versions - Latest release: 6 months ago - 5.37 thousand downloads total - 15 stars on GitHub - 1 maintainer
DepInfeR 1.6.0
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and...3 versions - Latest release: 6 months ago - 1.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
gwasurvivr 1.20.0
gwasurvivr: an R package for genome wide survival analysis3 versions - Latest release: 6 months ago - 9.71 thousand downloads total - 9 stars on GitHub - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...3 versions - Latest release: 7 months ago - 4.57 thousand downloads total - 0 stars on GitHub - 1 maintainer
oppti 1.16.0
Outlier Protein and Phosphosite Target Identifier3 versions - Latest release: 6 months ago - 4.61 thousand downloads total - 2 stars on GitHub - 1 maintainer
flowPloidy 1.28.0
Analyze flow cytometer data to determine sample ploidy3 versions - Latest release: 7 months ago - 10.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis2 versions - Latest release: 6 months ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
methylGSA 1.20.0
Gene Set Analysis Using the Outcome of Differential Methylation3 versions - Latest release: 7 months ago - 11.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
switchde 1.28.0
Switch-like differential expression across single-cell trajectories3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 19 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 26 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Cardinal 3.4.3
A mass spectrometry imaging toolbox for statistical analysis4 versions - Latest release: 6 months ago - 26.1 thousand downloads total - 1 maintainer
MetNet 1.20.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data3 versions - Latest release: 7 months ago - 6.9 thousand downloads total - 1 maintainer
pengls 1.8.0
Fit Penalised Generalised Least Squares models3 versions - Latest release: 7 months ago - 2.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
bacon 1.30.0
Controlling bias and inflation in association studies using the empirical null distribution3 versions - Latest release: 7 months ago - 16.9 thousand downloads total - 1 maintainer
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles3 versions - Latest release: 7 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
satuRn 1.10.0
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applic...3 versions - Latest release: 7 months ago - 1 dependent package - 7.57 thousand downloads total - 20 stars on GitHub - 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
graper 1.18.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...3 versions - Latest release: 7 months ago - 5.5 thousand downloads total - 1 maintainer
RLassoCox 1.10.0
A reweighted Lasso-Cox by integrating gene interaction information3 versions - Latest release: 7 months ago - 3.15 thousand downloads total - 3 stars on GitHub - 1 maintainer
anota2seq 1.24.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq3 versions - Latest release: 7 months ago - 11.1 thousand downloads total - 2 maintainers
chipenrich 2.26.0
Gene Set Enrichment For ChIP-seq Peak Data3 versions - Latest release: 7 months ago - 27.8 thousand downloads total - 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
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects3 versions - Latest release: 7 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer
LinkHD 1.16.0
LinkHD: a versatile framework to explore and integrate heterogeneous data3 versions - Latest release: 7 months ago - 4.84 thousand downloads total - 1 maintainer
CeTF 1.14.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...3 versions - Latest release: 7 months ago - 6.04 thousand downloads total - 1 maintainer
mirTarRnaSeq 1.10.0
mirTarRnaSeq3 versions - Latest release: 7 months ago - 3.38 thousand downloads total - 1 maintainer
sparsenetgls 1.20.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...3 versions - Latest release: 7 months ago - 5.7 thousand downloads total - 1 maintainer
hierinf 1.20.0
Hierarchical Inference3 versions - Latest release: 7 months ago - 5.33 thousand downloads total - 1 maintainer
gespeR 1.34.0
Gene-Specific Phenotype EstimatoR3 versions - Latest release: 7 months ago - 16.3 thousand downloads total - 1 maintainer
dmrseq 1.22.1
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing4 versions - Latest release: 2 months ago - 1 dependent package - 17.9 thousand downloads total - 1 maintainer
pareg 1.6.0
Pathway enrichment using a regularized regression approach3 versions - Latest release: 7 months ago - 1.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
GIGSEA 1.20.0
Genotype Imputed Gene Set Enrichment Analysis3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
fmrs 1.12.0
Variable Selection in Finite Mixture of AFT Regression and FMR Models3 versions - Latest release: 7 months ago - 5.47 thousand downloads total - 3 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
BioMM 1.18.0 removed
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using ...2 versions - Latest release: 7 months ago - 4.99 thousand downloads total - 1 maintainer
SIAMCAT 2.6.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 1 maintainer
CTSV 1.4.0
Identification of cell-type-specific spatially variable genes accounting for excess zeros3 versions - Latest release: 7 months ago - 1.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 7 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression3 versions - Latest release: 7 months ago - 22.2 thousand downloads total - 20 stars on GitHub - 2 maintainers
GAprediction 1.28.0
Prediction of gestational age with Illumina HumanMethylation450 data3 versions - Latest release: 7 months ago - 9.4 thousand downloads total - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity3 versions - Latest release: 7 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
IFAA 1.4.0
Robust Inference for Absolute Abundance in Microbiome Analysis3 versions - Latest release: 7 months ago - 1.54 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 51.9 thousand downloads total - 1 maintainer
gpls 1.74.0
Classification using generalized partial least squares3 versions - Latest release: 7 months ago - 1 dependent package - 51.9 thousand downloads total - 1 maintainer
rifi 1.6.0
'rifi' analyses data from rifampicin time series created by microarray or RNAseq3 versions - Latest release: 7 months ago - 1.71 thousand downloads total - 0 stars on GitHub - 1 maintainer
CytoDx 1.22.0
Robust prediction of clinical outcomes using cytometry data without cell gating3 versions - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 7 months ago - 7.55 thousand downloads total - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data4 versions - Latest release: about 1 month ago - 1 dependent package - 13 thousand downloads total - 118 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 7 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
kebabs 1.36.0
Kernel-Based Analysis of Biological Sequences3 versions - Latest release: 7 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Dino 1.8.0
Normalization of Single-Cell mRNA Sequencing Data3 versions - Latest release: 7 months ago - 2.77 thousand downloads total - 8 stars on GitHub - 1 maintainer
LRcell 1.10.0
Differential cell type change analysis using Logistic/linear Regression3 versions - Latest release: 7 months ago - 3.04 thousand downloads total - 3 stars on GitHub - 1 maintainer
GRaNIE 1.6.1
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...3 versions - Latest release: 7 months ago - 3.75 thousand downloads total - 1 maintainer
supersigs 1.10.0
Supervised mutational signatures3 versions - Latest release: 7 months ago - 2.71 thousand downloads total - 3 stars on GitHub - 1 maintainer
speckle 1.2.0
Statistical methods for analysing single cell RNA-seq data3 versions - Latest release: 7 months ago - 2.91 thousand downloads total - 1 maintainer
IMAS 1.26.0
Integrative analysis of Multi-omics data for Alternative Splicing3 versions - Latest release: 7 months ago - 9.74 thousand downloads total - 1 maintainer
GEM 1.28.0
GEM: fast association study for the interplay of Gene, Environment and Methylation3 versions - Latest release: 7 months ago - 10 thousand downloads total - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
BUMHMM 1.26.0
Computational pipeline for computing probability of modification from structure probing experimen...3 versions - Latest release: 7 months ago - 9.56 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 7 months ago - 5.54 thousand downloads total - 1 maintainer
xcore 1.6.0
xcore expression regulators inference3 versions - Latest release: 7 months ago - 1.9 thousand downloads total - 1 maintainer
weitrix 1.14.0
Tools for matrices with precision weights, test and explore weighted or sparse data3 versions - Latest release: 7 months ago - 4.22 thousand downloads total - 1 maintainer
globalSeq 1.30.0
Global Test for Counts3 versions - Latest release: 7 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
RNAdecay 1.22.2
Maximum Likelihood Decay Modeling of RNA Degradation Data5 versions - Latest release: 3 months ago - 5.73 thousand downloads total - 1 maintainer
CFAssay 1.36.0
Statistical analysis for the Colony Formation Assay3 versions - Latest release: 7 months ago - 15.4 thousand downloads total - 1 maintainer
AffiXcan 1.20.0
A Functional Approach To Impute Genetically Regulated Expression3 versions - Latest release: 7 months ago - 7.22 thousand downloads total - 1 maintainer
biotmle 1.26.0
Targeted Learning with Moderated Statistics for Biomarker Discovery3 versions - Latest release: 7 months ago - 10.6 thousand downloads total - 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
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
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
ENmix 1.38.01
Quality control and analysis tools for Illumina DNA methylation BeadChip3 versions - Latest release: 7 months ago - 27.6 thousand downloads total - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 7 months ago - 1.26 thousand downloads total - 1 maintainer
GNET2 1.18.0
Constructing gene regulatory networks from expression data through functional module inference3 versions - Latest release: 7 months ago - 5.66 thousand downloads total - 2 stars on GitHub - 1 maintainer
rnaEditr 1.12.0
Statistical analysis of RNA editing sites and hyper-editing regions3 versions - Latest release: 7 months ago - 3.35 thousand downloads total - 3 stars on GitHub - 1 maintainer
Related Keywords
Software
141
GeneExpression
72
DifferentialExpression
54
ImmunoOncology
51
RNASeq
51
Sequencing
44
Transcriptomics
38
MultipleComparison
28
Transcription
28
Normalization
26
SingleCell
25
Clustering
24
GeneRegulation
24
Epigenetics
24
Preprocessing
23
Microarray
22
Bayesian
22
Classification
21
TimeCourse
20
StatisticalMethod
20
Proteomics
20
GeneSetEnrichment
20
BatchEffect
19
Genetics
18
QualityControl
18
SystemsBiology
17
FunctionalGenomics
17
BiomedicalInformatics
17
DNAMethylation
15
SNP
14
DataImport
14
CellBiology
14
Survival
13
Network
13
Metabolomics
13
DimensionReduction
13
Visualization
13
GraphAndNetwork
12
DifferentialMethylation
12
Coverage
11
PrincipalComponent
11
FeatureExtraction
11
DifferentialSplicing
10
AlternativeSplicing
10
Pathways
9
MassSpectrometry
9
GenomeWideAssociation
9
ChIPSeq
8
mRNAMicroarray
7
MethylationArray
7
OneChannel
7
NetworkInference
7
r
6
TwoChannel
6
KEGG
6
bioconductor
6
ExperimentalDesign
6
GenePrediction
5
GeneTarget
5
CopyNumberVariation
5
CellBasedAssays
5
ProprietaryPlatforms
5
GeneticVariability
5
ExonArray
4
Lipidomics
4
GUI
4
Microbiome
4
Spatial
4
WholeGenome
4
Metagenomics
4
FlowCytometry
4
MethylSeq
3
Pharmacogenomics
3
DecisionTree
3
WorkflowStep
3
NetworkEnrichment
3
DataRepresentation
3
r-package
3
ATACSeq
3
GenomicVariation
3
FunctionalPrediction
3
MicroRNAArray
3
transcriptomics
3
shiny
2
rstats
2
miRNA
2
Annotation
2
GO
2
methylation
2
dna-methylation
2
Pharmacogenetics
2
TranscriptomeVariant
2
enrichment
2
regression
2
Cheminformatics
2
gene-expression
2
genomics
2
machine-learning
2
single-cell
2
negative-binomial
1