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
pengls 1.8.0
Fit Penalised Generalised Least Squares models3 versions - Latest release: 6 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: 6 months ago - 16.9 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
satuRn 1.10.0
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applic...3 versions - Latest release: 6 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: 6 months ago - 2 dependent packages - 8.57 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 15 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
graper 1.18.0
Adaptive penalization in high-dimensional regression and classification with external covariates ...3 versions - Latest release: 6 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: 6 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: 6 months ago - 11.1 thousand downloads total - 2 maintainers
chipenrich 2.26.0
Gene Set Enrichment For ChIP-seq Peak Data3 versions - Latest release: 6 months ago - 27.8 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
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
LinkHD 1.16.0
LinkHD: a versatile framework to explore and integrate heterogeneous data3 versions - Latest release: 6 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: 6 months ago - 6.04 thousand downloads total - 1 maintainer
mirTarRnaSeq 1.10.0
mirTarRnaSeq3 versions - Latest release: 6 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: 6 months ago - 5.7 thousand downloads total - 1 maintainer
hierinf 1.20.0
Hierarchical Inference3 versions - Latest release: 6 months ago - 5.33 thousand downloads total - 1 maintainer
gespeR 1.34.0
Gene-Specific Phenotype EstimatoR3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 months ago - 2.94 thousand downloads total - 4 stars on GitHub - 1 maintainer
pmm 1.34.0
Parallel Mixed Model3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression3 versions - Latest release: 6 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: 6 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: 6 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: 6 months ago - 1.54 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 3.75 thousand downloads total - 1 maintainer
supersigs 1.10.0
Supervised mutational signatures3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 9.56 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
xcore 1.6.0
xcore expression regulators inference3 versions - Latest release: 6 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: 6 months ago - 4.22 thousand downloads total - 1 maintainer
globalSeq 1.30.0
Global Test for Counts3 versions - Latest release: 6 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: 6 months ago - 15.4 thousand downloads total - 1 maintainer
AffiXcan 1.20.0
A Functional Approach To Impute Genetically Regulated Expression3 versions - Latest release: 6 months ago - 7.22 thousand downloads total - 1 maintainer
biotmle 1.26.0
Targeted Learning with Moderated Statistics for Biomarker Discovery3 versions - Latest release: 6 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: 6 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: 6 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: 6 months ago - 27.6 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
GNET2 1.18.0
Constructing gene regulatory networks from expression data through functional module inference3 versions - Latest release: 6 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: 6 months ago - 3.35 thousand downloads total - 3 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: 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
splineTimeR 1.30.0
Time-course differential gene expression data analysis using spline regression models followed by...3 versions - Latest release: 6 months ago - 12.4 thousand downloads total - 2 maintainers
pairkat 1.8.0
PaIRKAT3 versions - Latest release: 6 months ago - 2.16 thousand downloads total - 0 stars on GitHub - 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
Doscheda 1.24.0
A DownStream Chemo-Proteomics Analysis Pipeline3 versions - Latest release: 6 months ago - 8.5 thousand downloads total - 1 maintainer
GMRP 1.30.0
GWAS-based Mendelian Randomization and Path Analyses3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 maintainer
CONFESS 1.30.0
Cell OrderiNg by FluorEScence Signal3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 1 maintainer
IVAS 2.22.0
Identification of genetic Variants affecting Alternative Splicing3 versions - Latest release: 6 months ago - 1 dependent package - 14.4 thousand downloads total - 1 maintainer
consensus 1.20.0
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method3 versions - Latest release: 6 months ago - 6.17 thousand downloads total - 1 maintainer
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
airpart 1.10.0
Differential cell-type-specific allelic imbalance3 versions - Latest release: 6 months ago - 3.63 thousand downloads total - 2 stars on GitHub - 1 maintainer
trena 1.24.0 removed
Fit transcriptional regulatory networks using gene expression, priors, machine learning2 versions - Latest release: 6 months ago - 7 thousand downloads total - 1 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: 16 days ago - 1.21 thousand downloads total - 9 stars on GitHub - 1 maintainer
variancePartition 1.34.0
Quantify and interpret drivers of variation in multilevel gene expression experiments5 versions - Latest release: 15 days ago - 4 dependent packages - 57.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
NewWave 1.12.0
Negative binomial model for scRNA-seq3 versions - Latest release: 6 months ago - 5.06 thousand downloads total - 4 stars on GitHub - 1 maintainer
rqt 1.28.0
rqt: utilities for gene-level meta-analysis3 versions - Latest release: 6 months ago - 8.75 thousand downloads total - 2 stars on GitHub - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression6 versions - Latest release: 4 months ago - 1.2 thousand downloads total - 69 stars on GitHub - 1 maintainer
ExploreModelMatrix 1.16.0
Graphical Exploration of Design Matrices3 versions - Latest release: 6 days ago - 8.06 thousand downloads total - 36 stars on GitHub - 1 maintainer
topconfects 1.18.0
Top Confident Effect Sizes3 versions - Latest release: 6 months ago - 3 dependent packages - 10.8 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
4 versions - Latest release: 20 days ago - 146 dependent packages - 2.77 million downloads total - 328 stars on GitHub - 1 maintainer
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution4 versions - Latest release: 20 days ago - 146 dependent packages - 2.77 million downloads total - 328 stars on GitHub - 1 maintainer
transformGamPoi 1.10.0
Variance Stabilizing Transformation for Gamma-Poisson Models3 versions - Latest release: 7 days ago - 2.68 thousand downloads total - 18 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 4.3% on bioconductor.org
6 versions - Latest release: 7 days ago - 5 dependent packages - 147 thousand downloads total - 87 stars on GitHub - 1 maintainer
glmGamPoi 1.16.0
Fit a Gamma-Poisson Generalized Linear Model6 versions - Latest release: 7 days ago - 5 dependent packages - 147 thousand downloads total - 87 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
3 versions - Latest release: 7 days ago - 1 dependent package - 27.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
biobroom 1.36.0
Turn Bioconductor objects into tidy data frames3 versions - Latest release: 7 days ago - 1 dependent package - 27.3 thousand downloads total - 48 stars on GitHub - 1 maintainer
eisaR 1.16.0
Exon-Intron Split Analysis (EISA) in R4 versions - Latest release: 8 days ago - 7.62 thousand downloads total - 14 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
Top 2.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 9 dependent packages - 214 thousand downloads total - 1 maintainer
mixOmics 6.28.0
Omics Data Integration Project3 versions - Latest release: 13 days ago - 9 dependent packages - 214 thousand downloads total - 1 maintainer
msqrob2 1.12.0
Robust statistical inference for quantitative LC-MS proteomics3 versions - Latest release: 16 days ago - 5.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
MethReg 1.14.0
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription3 versions - Latest release: 11 days ago - 4.34 thousand downloads total - 4 stars on GitHub - 1 maintainer
POMA 1.14.0
Tools for Omics Data Analysis3 versions - Latest release: 11 days ago - 1 dependent package - 4.86 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 12 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: 12 days ago - 2 dependent packages - 73 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 48.9 thousand downloads total - 1 maintainer
limmaGUI 1.80.0
GUI for limma Package With Two Color Microarrays3 versions - Latest release: 13 days ago - 48.9 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 66 thousand downloads total - 1 maintainer
affylmGUI 1.78.0
GUI for limma Package with Affymetrix Microarrays3 versions - Latest release: 13 days ago - 66 thousand downloads total - 1 maintainer
timeOmics 1.16.0
Time-Course Multi-Omics data integration3 versions - Latest release: 13 days ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 98.3 thousand downloads total - 1 maintainer
GlobalAncova 4.22.0
Global test for groups of variables via model comparisons3 versions - Latest release: 13 days ago - 98.3 thousand downloads total - 1 maintainer
Related Keywords
Software
141
GeneExpression
72
DifferentialExpression
54
RNASeq
51
ImmunoOncology
51
Sequencing
44
Transcriptomics
38
MultipleComparison
28
Transcription
28
Normalization
26
SingleCell
25
GeneRegulation
24
Clustering
24
Epigenetics
24
Preprocessing
23
Bayesian
22
Microarray
22
Classification
21
Proteomics
20
GeneSetEnrichment
20
StatisticalMethod
20
TimeCourse
20
BatchEffect
19
QualityControl
18
Genetics
18
FunctionalGenomics
17
BiomedicalInformatics
17
SystemsBiology
17
DNAMethylation
15
SNP
14
CellBiology
14
DataImport
14
DimensionReduction
13
Metabolomics
13
Survival
13
Visualization
13
Network
13
GraphAndNetwork
12
DifferentialMethylation
12
Coverage
11
FeatureExtraction
11
PrincipalComponent
11
DifferentialSplicing
10
AlternativeSplicing
10
GenomeWideAssociation
9
Pathways
9
MassSpectrometry
9
ChIPSeq
8
OneChannel
7
MethylationArray
7
NetworkInference
7
mRNAMicroarray
7
TwoChannel
6
r
6
bioconductor
6
KEGG
6
ExperimentalDesign
6
GenePrediction
5
CopyNumberVariation
5
GeneticVariability
5
CellBasedAssays
5
GeneTarget
5
ProprietaryPlatforms
5
Spatial
4
FlowCytometry
4
ExonArray
4
Microbiome
4
Metagenomics
4
WholeGenome
4
Lipidomics
4
GUI
4
GenomicVariation
3
FunctionalPrediction
3
DataRepresentation
3
DecisionTree
3
r-package
3
MethylSeq
3
MicroRNAArray
3
transcriptomics
3
Pharmacogenomics
3
WorkflowStep
3
ATACSeq
3
NetworkEnrichment
3
Cheminformatics
2
shiny
2
dna-methylation
2
machine-learning
2
Pharmacogenetics
2
miRNA
2
genomics
2
GO
2
gene-expression
2
TranscriptomeVariant
2
Annotation
2
regression
2
single-cell
2
enrichment
2
bioconductor-package
1
rnaseq
1
salmon
1