Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "GeneRegulation" keyword
MIRA 1.24.0
Methylation-Based Inference of Regulatory Activity3 versions - Latest release: 6 months ago - 1 dependent package - 10.5 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
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 6 months ago - 3 dependent packages - 23.4 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
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 7 dependent packages - 57.3 thousand downloads total - 1 maintainer
viper 1.36.0
Virtual Inference of Protein-activity by Enriched Regulon analysis3 versions - Latest release: 6 months ago - 7 dependent packages - 57.3 thousand downloads total - 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
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
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 6 months ago - 9.18 thousand downloads total - 1 maintainer
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression3 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
nullranges 1.8.0
Generation of null ranges via bootstrapping or covariate matching3 versions - Latest release: 6 months ago - 1 dependent package - 4.44 thousand downloads total - 22 stars on GitHub - 1 maintainer
BiFET 1.22.0
Bias-free Footprint Enrichment Test3 versions - Latest release: 6 months ago - 8.91 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 38 thousand downloads total - 1 maintainer
ELMER 2.26.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes3 versions - Latest release: 6 months ago - 38 thousand downloads total - 1 maintainer
BasicSTARRseq 1.30.0
Basic peak calling on STARR-seq data3 versions - Latest release: 6 months ago - 12 thousand downloads total - 1 maintainer
MatrixRider 1.34.0
Obtain total affinity and occupancies for binding site matrices on a given sequence3 versions - Latest release: 6 months ago - 12.6 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
RTN 2.26.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons3 versions - Latest release: 6 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
SEPIRA 1.22.0 removed
Systems EPigenomics Inference of Regulatory Activity2 versions - Latest release: 6 months ago - 5.66 thousand downloads total - 1 maintainer
idr2d 1.16.0
Irreproducible Discovery Rate for Genomic Interactions Data3 versions - Latest release: 6 months ago - 5.25 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
sRACIPE 1.18.0
Systems biology tool to simulate gene regulatory circuits3 versions - Latest release: 6 months ago - 5.77 thousand downloads total - 0 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
GSRI 2.50.0
Gene Set Regulation Index3 versions - Latest release: 6 months ago - 25.8 thousand downloads total - 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
CRISPRseek 1.42.0
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems3 versions - Latest release: 6 months ago - 3 dependent packages - 28.9 thousand downloads total - 1 maintainer
ribosomeProfilingQC 1.14.1
Ribosome Profiling Quality Control4 versions - Latest release: about 1 month ago - 5.54 thousand downloads total - 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
mpra 1.24.0
Analyze massively parallel reporter assays3 versions - Latest release: 6 months ago - 8.48 thousand downloads total - 5 stars on GitHub - 1 maintainer
proActiv 1.12.0
Estimate Promoter Activity from RNA-Seq data3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 44 stars on GitHub - 1 maintainer
LOLA 1.32.0
Locus overlap analysis for enrichment of genomic ranges3 versions - Latest release: 6 months ago - 5 dependent packages - 25 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
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
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
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
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
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
Cogito 1.8.0
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic...3 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 1 maintainer
BRGenomics 1.14.1
Tools for the Efficient Analysis of High-Resolution Genomics Data4 versions - Latest release: 2 months ago - 1 dependent package - 8.07 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
GRENITS 1.54.0
Gene Regulatory Network Inference Using Time Series3 versions - Latest release: 6 months ago - 23.6 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
CoRegNet 1.40.0
CoRegNet : reconstruction and integrated analysis of co-regulatory networks3 versions - Latest release: 6 months ago - 16.9 thousand downloads total - 1 maintainer
rifiComparative 1.2.0
'rifiComparative' compares the output of rifi from two different conditions.3 versions - Latest release: 6 months ago - 1.11 thousand downloads total - 0 stars on GitHub - 1 maintainer
universalmotif 1.20.0
Import, Modify, and Export Motifs with R3 versions - Latest release: 6 months ago - 4 dependent packages - 28.5 thousand downloads total - 1 maintainer
blima 1.36.0
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level3 versions - Latest release: 6 months ago - 15.9 thousand downloads total - 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
Top 9.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 36.7 thousand downloads total - 1 maintainer
BCRANK 1.64.0
Predicting binding site consensus from ranked DNA sequences3 versions - Latest release: 6 months ago - 36.7 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
spatzie 1.8.0
Identification of enriched motif pairs from chromatin interaction data3 versions - Latest release: 6 months ago - 2.36 thousand downloads total - 1 maintainer
BindingSiteFinder 2.0.0
Binding site defintion based on iCLIP data3 versions - Latest release: 6 months ago - 2.89 thousand downloads total - 3 stars on GitHub - 1 maintainer
SELEX 1.34.0
Functions for analyzing SELEX-seq data3 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 1 maintainer
INSPEcT 1.32.1
Modeling RNA synthesis, processing and degradation with RNA-seq data4 versions - Latest release: 4 months ago - 14.3 thousand downloads total - 2 maintainers
eegc 1.28.0
Engineering Evaluation by Gene Categorization (eegc)3 versions - Latest release: 6 months ago - 9.92 thousand downloads total - 1 maintainer
StarBioTrek 1.28.0
StarBioTrek3 versions - Latest release: 6 months ago - 10 thousand downloads total - 0 stars on GitHub - 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
RTNsurvival 1.26.0
Survival analysis using transcriptional networks inferred by the RTN package3 versions - Latest release: 6 months ago - 8.93 thousand downloads total - 2 maintainers
RTNduals 1.26.0
Analysis of co-regulation and inference of 'dual regulons'3 versions - Latest release: 6 months ago - 1 dependent package - 10.1 thousand downloads total - 2 maintainers
NADfinder 1.26.0
Call wide peaks for sequencing data3 versions - Latest release: 6 months ago - 9.86 thousand downloads total - 2 maintainers
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
TFEA.ChIP 1.22.0
Analyze Transcription Factor Enrichment3 versions - Latest release: 6 months ago - 8.82 thousand downloads total - 1 maintainer
IntOMICS 1.2.0
Integrative analysis of multi-omics data to infer regulatory networks3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 0 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
geneplast 1.28.0
Evolutionary and plasticity analysis of orthologous groups3 versions - Latest release: 6 months ago - 1 dependent package - 10.8 thousand downloads total - 1 maintainer
sarks 1.14.0
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains3 versions - Latest release: 6 months ago - 4.04 thousand downloads total - 1 maintainer
triplex 1.42.0
Search and visualize intramolecular triplex-forming sequences in DNA3 versions - Latest release: 6 months ago - 19.7 thousand downloads total - 1 maintainer
ATACseqQC 1.26.0
ATAC-seq Quality Control3 versions - Latest release: 6 months ago - 2 dependent packages - 42.4 thousand downloads total - 1 maintainer
GSReg 1.36.0
Gene Set Regulation (GS-Reg)3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 2 maintainers
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
GUIDEseq 1.32.0
GUIDE-seq and PEtag-seq analysis pipeline3 versions - Latest release: 6 months ago - 1 dependent package - 14.3 thousand downloads total - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 6 months ago - 7.09 thousand downloads total - 1 maintainer
cicero 1.20.0
Predict cis-co-accessibility from single-cell chromatin accessibility data3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 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
tRanslatome 1.40.0
Comparison between multiple levels of gene expression3 versions - Latest release: 6 months ago - 20 thousand downloads total - 2 maintainers
pqsfinder 2.18.0
Identification of potential quadruplex forming sequences3 versions - Latest release: 6 months ago - 13.3 thousand downloads total - 1 maintainer
DeepBlueR 1.27.0 removed
DeepBlueR2 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 3 maintainers
Top 1.8% on bioconductor.org
4 versions - Latest release: 16 days ago - 14 dependent packages - 312 thousand downloads total - 2 maintainers
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data4 versions - Latest release: 16 days ago - 14 dependent packages - 312 thousand downloads total - 2 maintainers
progeny 1.26.0
Pathway RespOnsive GENes for activity inference from gene expression3 versions - Latest release: 7 days ago - 2 dependent packages - 26.5 thousand downloads total - 88 stars on GitHub - 1 maintainer
decoupleR 2.9.7
decoupleR: Ensemble of computational methods to infer biological activities from omics data3 versions - Latest release: 7 days ago - 3 dependent packages - 25.4 thousand downloads total - 154 stars on GitHub - 1 maintainer
MoonlightR 1.30.0
Identify oncogenes and tumor suppressor genes from omics data3 versions - Latest release: 20 days ago - 11.7 thousand downloads total - 17 stars on GitHub - 1 maintainer
PIPETS 1.0.0
Poisson Identification of PEaks from Term-Seq data1 version - Latest release: 21 days ago - 293 downloads total - 0 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
netZooR 1.8.0
Unified methods for the inference and analysis of gene regulatory networks3 versions - Latest release: 8 days ago - 2.36 thousand downloads total - 84 stars on GitHub - 1 maintainer
projectR 1.20.0
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering3 versions - Latest release: 8 days ago - 1 dependent package - 7.22 thousand downloads total - 62 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
4 versions - Latest release: 12 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
TCGAbiolinks 2.32.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data4 versions - Latest release: 12 days ago - 7 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
epiregulon 1.0.0
Gene regulatory network inference from single cell epigenomic data1 version - Latest release: 21 days ago - 1 dependent package - 12 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 12 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 13 days ago - 17 dependent packages - 288 thousand downloads total - 23 stars on GitHub - 1 maintainer
TFBSTools 1.42.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis3 versions - Latest release: 13 days ago - 17 dependent packages - 288 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 85.1 thousand downloads total - 1 maintainer
chromVAR 1.26.0
Chromatin Variation Across Regions3 versions - Latest release: 13 days ago - 1 dependent package - 85.1 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 198 thousand downloads total - 3 stars on GitHub - 1 maintainer
CNEr 1.40.0
CNE Detection and Visualization3 versions - Latest release: 13 days ago - 1 dependent package - 198 thousand downloads total - 3 stars on GitHub - 1 maintainer
rTRMui 1.42.0
A shiny user interface for rTRM3 versions - Latest release: 13 days ago - 16.7 thousand downloads total - 1 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
Top 3.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 77.5 thousand downloads total - 1 maintainer
RcisTarget 1.24.0
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic re...3 versions - Latest release: 13 days ago - 77.5 thousand downloads total - 1 maintainer
memes 1.12.0
motif matching, comparison, and de novo discovery using the MEME Suite3 versions - Latest release: 13 days ago - 8.72 thousand downloads total - 43 stars on GitHub - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus5 versions - Latest release: 14 days ago - 1 dependent package - 8.17 thousand downloads total - 17 stars on GitHub - 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
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements3 versions - Latest release: 16 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
ATACseqTFEA 1.6.0
Transcription Factor Enrichment Analysis for ATAC-seq3 versions - Latest release: 16 days ago - 1.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software
118
GeneExpression
66
Transcription
42
Sequencing
40
DifferentialExpression
31
RNASeq
29
Network
27
ImmunoOncology
26
SystemsBiology
24
Regression
24
FunctionalGenomics
23
Transcriptomics
21
GeneSetEnrichment
20
NetworkInference
20
Epigenetics
19
Genetics
16
GraphAndNetwork
16
Microarray
14
Coverage
14
DNAMethylation
13
Pathways
12
ATACSeq
12
ChIPSeq
12
GeneTarget
11
DataImport
11
Bayesian
10
SingleCell
10
Visualization
10
Normalization
10
Preprocessing
10
Clustering
10
DifferentialMethylation
10
NetworkEnrichment
10
FunctionalPrediction
9
SNP
8
MotifDiscovery
8
QualityControl
8
r
7
Annotation
7
GenomeAnnotation
7
GeneticVariability
7
PeakDetection
7
MotifAnnotation
7
FeatureExtraction
7
MultipleComparison
6
KEGG
6
AlternativeSplicing
6
StatisticalMethod
6
SequenceMatching
6
MethylationArray
6
BiomedicalInformatics
5
DNaseSeq
5
Survival
5
TimeCourse
5
DifferentialSplicing
4
Alignment
4
bioconductor
4
MethylSeq
4
DNASeq
4
genomics
4
CellBiology
4
PrincipalComponent
3
WorkflowStep
3
Classification
3
HistoneModification
3
GenomicVariation
3
BatchEffect
3
GenomeWideAssociation
3
GO
3
MathematicalBiology
3
CopyNumberVariation
3
DataRepresentation
3
clustering
2
TranscriptomeVariant
2
Proteomics
2
DimensionReduction
2
r-package
2
CRISPR
2
rstats
2
VariantAnnotation
2
RiboSeq
2
ThirdPartyClient
2
ChipOnChip
2
bioinformatics
2
HiddenMarkovModel
2
RIPSeq
2
DNA3DStructure
2
HiC
2
genetics
2
cerna
1
miRNA
1
GenomeBrowsers
1
ReportWriting
1
DifferentialPeakCalling
1
GUI
1
intermine
1
biology
1
enrichment
1
generalized-linear-models
1
logistic-regression
1