Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "DifferentialExpression" keyword
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...6 versions - Latest release: 6 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
2 versions - Latest release: 6 months ago - 29.9 thousand downloads total - 1 maintainer
macat 1.76.0 removed
MicroArray Chromosome Analysis Tool2 versions - Latest release: 6 months ago - 29.9 thousand downloads total - 1 maintainer
RiboDiPA 1.10.0
Differential pattern analysis for Ribo-seq data3 versions - Latest release: 6 months ago - 3.28 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 months ago - 6.29 thousand downloads total - 1 maintainer
epidecodeR 1.10.0
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation3 versions - Latest release: 6 months ago - 2.79 thousand downloads total - 3 stars on GitHub - 1 maintainer
APAlyzer 1.16.0
A toolkit for APA analysis using RNA-seq data3 versions - Latest release: 6 months ago - 6.99 thousand downloads total - 4 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: 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
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
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 34.6 thousand downloads total - 1 maintainer
factDesign 1.78.0
Factorial designed microarray experiment analysis3 versions - Latest release: 6 months ago - 34.6 thousand downloads total - 1 maintainer
MODA 1.28.0
MODA: MOdule Differential Analysis for weighted gene co-expression network3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
mAPKL 1.32.0 removed
A Hybrid Feature Selection method for gene expression data2 versions - Latest release: 6 months ago - 11.8 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
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
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
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
Linnorm 2.26.0
Linear model and normality based normalization and transformation method (Linnorm)3 versions - Latest release: 6 months ago - 1 dependent package - 22.4 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
HEM 1.74.0
Heterogeneous error model for identification of differentially expressed genes under multiple con...3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
plgem 1.74.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas3 versions - Latest release: 15 days ago - 1.07 thousand downloads total - 77 stars on GitHub - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
TOAST 1.16.0
Tools for the analysis of heterogeneous tissues3 versions - Latest release: 6 months ago - 3 dependent packages - 15.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
anota 1.50.0
ANalysis Of Translational Activity (ANOTA).3 versions - Latest release: 6 months ago - 1 dependent package - 29.3 thousand downloads total - 1 maintainer
scDD 1.26.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions3 versions - Latest release: 6 months ago - 1 dependent package - 19.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
epigenomix 1.42.0
Epigenetic and gene transcription data normalization and integration with mixture models3 versions - Latest release: 6 months ago - 20.6 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 33.1 thousand downloads total - 1 maintainer
miRNApath 1.62.0
miRNApath: Pathway Enrichment for miRNA Expression Data3 versions - Latest release: 6 months ago - 33.1 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data3 versions - Latest release: 13 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
BioNet 1.62.0
Routines for the functional analysis of biological networks3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data3 versions - Latest release: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq3 versions - Latest release: 6 months ago - 3 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
EBSEA 1.30.0
Exon Based Strategy for Expression Analysis of genes3 versions - Latest release: 6 months ago - 10.1 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 29.6 thousand downloads total - 1 maintainer
GeneSelectMMD 2.46.0
Gene selection based on the marginal distributions of gene profiles that characterized by a mixtu...3 versions - Latest release: 6 months ago - 1 dependent package - 29.6 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
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
crossmeta 1.28.0
Cross Platform Meta-Analysis of Microarray Data3 versions - Latest release: 6 months ago - 1 dependent package - 15.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
IntEREst 1.26.0
Intron-Exon Retention Estimator3 versions - Latest release: 6 months ago - 11 thousand downloads total - 2 maintainers
geva 1.10.0
Gene Expression Variation Analysis (GEVA)3 versions - Latest release: 6 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
ISLET 1.4.0
Individual-Specific ceLl typE referencing Tool3 versions - Latest release: 6 months ago - 1.63 thousand downloads total - 1 maintainer
consensusOV 1.24.0
Gene expression-based subtype classification for high-grade serous ovarian cancer3 versions - Latest release: 6 months ago - 1 dependent package - 9.83 thousand downloads total - 1 maintainer
Top 7.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 38.2 thousand downloads total - 1 maintainer
ddCt 1.58.0
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)3 versions - Latest release: 6 months ago - 38.2 thousand downloads total - 1 maintainer
MetaVolcanoR 1.16.0
Gene Expression Meta-analysis Visualization Tool3 versions - Latest release: 6 months ago - 10.5 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
ppcseq 1.10.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models3 versions - Latest release: 6 months ago - 2.85 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 27.4 thousand downloads total - 1 maintainer
pickgene 1.74.0
Adaptive Gene Picking for Microarray Expression Data Analysis3 versions - Latest release: 6 months ago - 27.4 thousand downloads total - 1 maintainer
DART 1.50.0
Denoising Algorithm based on Relevance network Topology3 versions - Latest release: 6 months ago - 24 thousand downloads total - 1 maintainer
TTMap 1.24.0
Two-Tier Mapper: a clustering tool based on topological data analysis3 versions - Latest release: 6 months ago - 6.96 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
metahdep 1.60.0
Hierarchical Dependence in Meta-Analysis3 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
CONSTANd 1.10.0
Data normalization by matrix raking3 versions - Latest release: 6 months ago - 3.41 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 33 thousand downloads total - 1 maintainer
copa 1.70.0
Functions to perform cancer outlier profile analysis.3 versions - Latest release: 6 months ago - 33 thousand downloads total - 1 maintainer
NanoStringDiff 1.32.0
Differential Expression Analysis of NanoString nCounter Data3 versions - Latest release: 6 months ago - 1 dependent package - 16.4 thousand downloads total - 2 maintainers
Top 6.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
HTSFilter 1.42.0
Filter replicated high-throughput transcriptome sequencing data3 versions - Latest release: 6 months ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
Moonlight2R 1.2.0
Identify oncogenes and tumor suppressor genes from omics data2 versions - Latest release: 20 days ago - 1.06 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 38.1 thousand downloads total - 1 maintainer
LPE 1.76.0
Methods for analyzing microarray data using Local Pooled Error (LPE) method3 versions - Latest release: 6 months ago - 3 dependent packages - 38.1 thousand downloads total - 1 maintainer
NanoTube 1.8.0
An Easy Pipeline for NanoString nCounter Data Analysis3 versions - Latest release: 6 months ago - 3.18 thousand downloads total - 1 maintainer
similaRpeak 1.34.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles3 versions - Latest release: 6 months ago - 1 dependent package - 14 thousand downloads total - 7 stars on GitHub - 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
geNetClassifier 1.42.0
Classify diseases and build associated gene networks using gene expression profiles3 versions - Latest release: 6 months ago - 2 dependent packages - 26.2 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 36.5 thousand downloads total - 1 maintainer
DeconRNASeq 1.44.0
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data3 versions - Latest release: 6 months ago - 36.5 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
XDE 2.48.0
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
lmdme 1.44.0
Linear Model decomposition for Designed Multivariate Experiments3 versions - Latest release: 6 months ago - 21.4 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
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
CAEN 1.10.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq3 versions - Latest release: 6 months ago - 2.78 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
DRIMSeq 1.30.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
omicplotR 1.22.0
Visual Exploration of Omic Datasets Using a Shiny App3 versions - Latest release: 6 months ago - 8.13 thousand downloads total - 1 maintainer
ROTS 1.30.0
Reproducibility-Optimized Test Statistic3 versions - Latest release: 6 months ago - 2 dependent packages - 23.4 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
GIGSEA 1.20.0
Genotype Imputed Gene Set Enrichment Analysis3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets3 versions - Latest release: 6 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
coGPS 1.46.0
cancer outlier Gene Profile Sets3 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 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
GSRI 2.50.0
Gene Set Regulation Index3 versions - Latest release: 6 months ago - 25.8 thousand downloads total - 1 maintainer
PECA 1.38.0
Probe-level Expression Change Averaging3 versions - Latest release: 6 months ago - 1 dependent package - 17.8 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays3 versions - Latest release: 6 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
DFP 1.60.0
Gene Selection3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
FoldGO 1.20.0
Package for Fold-specific GO Terms Recognition3 versions - Latest release: 6 months ago - 5.5 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
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
aggregateBioVar 1.12.0
Differential Gene Expression Analysis for Multi-subject scRNA-seq3 versions - Latest release: 6 months ago - 5.15 thousand downloads total - 5 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
RnaSeqSampleSize 2.12.0
RnaSeqSampleSize3 versions - Latest release: 6 months ago - 16.8 thousand downloads total - 1 maintainer
TBSignatureProfiler 1.14.0
Profile RNA-Seq Data Using TB Pathway Signatures3 versions - Latest release: 6 months ago - 4.74 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 32.2 thousand downloads total - 1 maintainer
gaga 2.48.0
GaGa hierarchical model for high-throughput data analysis3 versions - Latest release: 6 months ago - 1 dependent package - 32.2 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
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
Top 9.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 2 maintainers
polyester 1.38.0
Simulate RNA-seq reads3 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 2 maintainers
ERSSA 1.20.0
Empirical RNA-seq Sample Size Analysis3 versions - Latest release: 6 months ago - 6.38 thousand downloads total - 0 stars on GitHub - 1 maintainer
MetaPhOR 1.4.0
Metabolic Pathway Analysis of RNA3 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
DEP 1.24.0
Differential Enrichment analysis of Proteomics data3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 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
iGC 1.32.0
An integrated analysis package of Gene expression and Copy number alteration3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
DEsubs 1.28.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 maintainers
ASpli 2.12.0
Analysis of Alternative Splicing Using RNA-Seq3 versions - Latest release: 6 months ago - 1 dependent package - 17 thousand downloads total - 1 maintainer
CellTrails 1.20.0
Reconstruction, visualization and analysis of branching trajectories3 versions - Latest release: 6 months ago - 6.81 thousand downloads total - 1 maintainer
GSALightning 1.30.0
Fast Permutation-based Gene Set Analysis3 versions - Latest release: 6 months ago - 10.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
GCSscore 1.16.0 removed
GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays2 versions - Latest release: 6 months ago - 4.11 thousand downloads total - 1 maintainer
Related Keywords
Software
388
GeneExpression
239
RNASeq
174
Sequencing
143
ImmunoOncology
131
Microarray
121
Transcription
75
MultipleComparison
75
Transcriptomics
75
Visualization
73
Clustering
68
Normalization
67
GeneSetEnrichment
63
Regression
54
QualityControl
51
Preprocessing
51
SingleCell
50
StatisticalMethod
43
Proteomics
42
Network
39
Pathways
39
DataImport
34
Genetics
32
Bayesian
32
GeneRegulation
31
Classification
29
OneChannel
29
TimeCourse
29
SystemsBiology
28
bioconductor
28
DifferentialSplicing
28
AlternativeSplicing
27
Coverage
26
GraphAndNetwork
25
r
25
BatchEffect
24
TwoChannel
21
MassSpectrometry
21
FunctionalGenomics
21
BiomedicalInformatics
20
NetworkEnrichment
20
DifferentialMethylation
20
GO
18
Epigenetics
17
DNAMethylation
16
Metabolomics
15
mRNAMicroarray
15
CellBiology
15
GUI
14
ChIPSeq
13
Infrastructure
12
SNP
12
DataRepresentation
12
PrincipalComponent
12
GeneTarget
11
DimensionReduction
11
KEGG
11
ExonArray
11
ReportWriting
11
Annotation
11
ExperimentalDesign
11
bioconductor-package
10
rstats
9
Survival
9
FeatureExtraction
9
rna-seq
9
NetworkInference
9
Alignment
9
gene-expression
9
MethylationArray
9
transcriptomics
8
Microbiome
8
FunctionalPrediction
8
GenomeAnnotation
8
differential-expression
8
rnaseq
7
MicroRNAArray
6
single-cell
6
WorkflowStep
6
derfinder
6
CopyNumberVariation
6
ProprietaryPlatforms
6
Metagenomics
6
GenomeWideAssociation
6
AssayDomain
6
BiologicalQuestion
5
single-cell-rna-seq
5
genomics
5
ShinyApps
5
miRNA
5
FlowCytometry
5
ATACSeq
5
DNASeq
5
bioinformatics
5
deseq2
5
rna-seq-analysis
4
GenomicVariation
4
SAGE
4
r-package
4
GeneSignaling
3