Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "ChIPSeq" 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
dpeak 1.14.0
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)3 versions - Latest release: 6 months ago - 6.07 thousand downloads total - 0 stars on GitHub - 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
TransView 1.46.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets3 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 1 maintainer
MACSr 1.10.0
MACS: Model-based Analysis for ChIP-Seq3 versions - Latest release: 6 months ago - 5.49 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
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
ChIPXpress 1.46.0
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip ...3 versions - Latest release: 6 months ago - 16.7 thousand downloads total - 1 maintainer
epigraHMM 1.10.0
Epigenomic R-based analysis with hidden Markov models3 versions - Latest release: 6 months ago - 3.3 thousand downloads total - 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
BaalChIP 1.28.0
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 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 2.9% on bioconductor.org
3 versions - Latest release: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data3 versions - Latest release: 18 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 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
InTAD 1.22.0
Search for correlation between epigenetic signals and gene expression in TADs3 versions - Latest release: 6 months ago - 7.87 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
Top 6.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 58.3 thousand downloads total - 2 maintainers
ChIPQC 1.38.0
Quality metrics for ChIPseq data3 versions - Latest release: 6 months ago - 58.3 thousand downloads total - 2 maintainers
marr 1.12.0
Maximum rank reproducibility3 versions - Latest release: 6 months ago - 3.29 thousand downloads total - 2 stars on GitHub - 1 maintainer
atSNP 1.18.0
Affinity test for identifying regulatory SNPs3 versions - Latest release: 6 months ago - 6.67 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 38.3 thousand downloads total - 1 maintainer
ChIPsim 1.56.0
Simulation of ChIP-seq experiments3 versions - Latest release: 6 months ago - 38.3 thousand downloads total - 1 maintainer
CSSP 1.40.0 removed
ChIP-Seq Statistical Power2 versions - Latest release: 6 months ago - 17.8 thousand downloads total
TFHAZ 1.24.0
Transcription Factor High Accumulation Zones3 versions - Latest release: 6 months ago - 7.41 thousand downloads total - 1 maintainer
MMDiff2 1.30.0
Statistical Testing for ChIP-Seq data sets3 versions - Latest release: 6 months ago - 10.5 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
ChIPexoQual 1.26.0
ChIPexoQual3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 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
soGGi 1.34.0
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Gen...3 versions - Latest release: 6 months ago - 1 dependent package - 26.7 thousand downloads total - 1 maintainer
CexoR 1.40.0
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates3 versions - Latest release: 6 months ago - 18.6 thousand downloads total - 1 maintainer
RepViz 1.18.0
Replicate oriented Visualization of a genomic region3 versions - Latest release: 6 months ago - 6.28 thousand downloads total - 1 maintainer
qsea 1.28.0
IP-seq data analysis and vizualization3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 39.6 thousand downloads total - 1 maintainer
ChIPseqR 1.56.0
Identifying Protein Binding Sites in High-Throughput Sequencing Data3 versions - Latest release: 6 months ago - 39.6 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
wiggleplotr 1.26.0
Make read coverage plots from BigWig files3 versions - Latest release: 6 months ago - 1 dependent package - 14.7 thousand downloads total - 1 maintainer
Motif2Site 1.6.0
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across condi...3 versions - Latest release: 6 months ago - 2.02 thousand downloads total - 0 stars on GitHub - 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
LedPred 1.36.0
Learning from DNA to Predict Enhancers3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 1 maintainer
gcapc 1.26.0
GC Aware Peak Caller3 versions - Latest release: 6 months ago - 1 dependent package - 9.54 thousand downloads total - 9 stars on GitHub - 1 maintainer
TCseq 1.26.0
Time course sequencing data analysis3 versions - Latest release: 6 months ago - 16.3 thousand downloads total - 1 maintainer
normr 1.28.0
Normalization and difference calling in ChIP-seq data3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
cliProfiler 1.8.0
A package for the CLIP data visualization3 versions - Latest release: 6 months ago - 2.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 38.9 thousand downloads total - 1 maintainer
CSAR 1.54.0
Statistical tools for the analysis of ChIP-seq data3 versions - Latest release: 6 months ago - 38.9 thousand downloads total - 1 maintainer
ChIPComp 1.32.0
Quantitative comparison of multiple ChIP-seq datasets3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 maintainer
CoverageView 1.40.0
Coverage visualization package for R3 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 1 maintainer
consensusSeekeR 1.30.0
Detection of consensus regions inside a group of experiences using genomic positions and genomic ...3 versions - Latest release: 6 months ago - 2 dependent packages - 12.7 thousand downloads total - 1 stars on GitHub - 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
ChIPanalyser 1.24.0
ChIPanalyser: Predicting Transcription Factor Binding Sites3 versions - Latest release: 6 months ago - 8.35 thousand downloads total - 1 maintainer
iASeq 1.46.0
iASeq: integrating multiple sequencing datasets for detecting allele-specific events3 versions - Latest release: 6 months ago - 21.2 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
epistack 1.8.0
Heatmaps of Stack Profiles from Epigenetic Signals3 versions - Latest release: 6 months ago - 2.46 thousand downloads total - 6 stars on GitHub - 1 maintainer
fCCAC 1.28.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...3 versions - Latest release: 6 months ago - 9.84 thousand downloads total - 1 maintainer
seqsetvis 1.22.1
Set Based Visualizations for Next-Gen Sequencing Data4 versions - Latest release: 2 months ago - 8.78 thousand downloads total - 1 maintainer
vulcan 1.24.0
VirtUaL ChIP-Seq data Analysis using Networks3 versions - Latest release: 6 months ago - 8.7 thousand downloads total - 1 maintainer
CSSQ 1.14.0
Chip-seq Signal Quantifier Pipeline3 versions - Latest release: 6 months ago - 4.31 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
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
coMET 1.34.0
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methyl...3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 1 maintainer
profileplyr 1.18.0
Visualization and annotation of read signal over genomic ranges with profileplyr3 versions - Latest release: 6 months ago - 1 dependent package - 13.7 thousand downloads total - 2 maintainers
extraChIPs 1.8.1
Additional functions for working with ChIP-Seq data5 versions - Latest release: 13 days ago - 2 dependent packages - 2.54 thousand downloads total - 7 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
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
sitadela 1.12.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...3 versions - Latest release: 8 days ago - 2.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
recoup 1.32.0
An R package for the creation of complex genomic profile plots3 versions - Latest release: 8 days ago - 10.9 thousand downloads total - 1 stars on GitHub - 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
GenomicPlot 1.2.0
Plot profiles of next generation sequencing data in genomic features9 versions - Latest release: 9 days ago - 1.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
3 versions - Latest release: 13 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
regioneR 1.36.0
Association analysis of genomic regions based on permutation tests3 versions - Latest release: 13 days ago - 13 dependent packages - 217 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
3 versions - Latest release: 12 days ago - 10 dependent packages - 106 thousand downloads total - 1 maintainer
motifStack 1.48.0
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence3 versions - Latest release: 12 days ago - 10 dependent packages - 106 thousand downloads total - 1 maintainer
HicAggR 1.0.0
Set of 3D genomic interaction analysis tools1 version - Latest release: 21 days ago - 82 downloads total - 0 stars on GitHub - 1 maintainer
Top 3.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 2 dependent packages - 92.3 thousand downloads total - 1 maintainer
QuasR 1.44.0
Quantify and Annotate Short Reads in R3 versions - Latest release: 13 days ago - 2 dependent packages - 92.3 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
4 versions - Latest release: 13 days ago - 8 dependent packages - 72.1 thousand downloads total - 1 maintainer
csaw 1.38.0
ChIP-Seq Analysis with Windows4 versions - Latest release: 13 days ago - 8 dependent packages - 72.1 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
chipseq 1.54.0
chipseq: A package for analyzing chipseq data3 versions - Latest release: 13 days ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
Top 3.4% on bioconductor.org
3 versions - Latest release: 13 days ago - 1 dependent package - 89.7 thousand downloads total - 1 maintainer
rGADEM 2.52.0
de novo motif discovery3 versions - Latest release: 13 days ago - 1 dependent package - 89.7 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
3 versions - Latest release: 13 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
systemPipeR 2.10.0
systemPipeR: workflow management and report generation environment3 versions - Latest release: 13 days ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
3 versions - Latest release: 13 days ago - 48.6 thousand downloads total - 1 maintainer
MEDIPS 1.56.0
DNA IP-seq data analysis3 versions - Latest release: 13 days ago - 48.6 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: 13 days ago - 2 dependent packages - 60.6 thousand downloads total - 1 maintainer
GreyListChIP 1.36.0
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs3 versions - Latest release: 13 days ago - 2 dependent packages - 60.6 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
4 versions - Latest release: 13 days ago - 8 dependent packages - 267 thousand downloads total - 4 maintainers
ChIPpeakAnno 3.38.0
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any expe...4 versions - Latest release: 13 days ago - 8 dependent packages - 267 thousand downloads total - 4 maintainers
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 3.3% on bioconductor.org
3 versions - Latest release: 13 days ago - 6 dependent packages - 232 thousand downloads total - 1 maintainer
ChIPseeker 1.40.0
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization3 versions - Latest release: 13 days ago - 6 dependent packages - 232 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
5 versions - Latest release: 16 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
debrowser 1.32.0
Interactive Differential Expresion Analysis Browser5 versions - Latest release: 16 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
motifTestR 1.0.0
Perform key tests for binding motifs in sequence data1 version - Latest release: 21 days ago - 179 downloads total - 0 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
3 versions - Latest release: 19 days ago - 6 dependent packages - 67.7 thousand downloads total - 42 stars on GitHub - 1 maintainer
derfinder 1.38.0
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via ...3 versions - Latest release: 19 days ago - 6 dependent packages - 67.7 thousand downloads total - 42 stars on GitHub - 1 maintainer
DegCre 1.0.0
Probabilistic association of DEGs to CREs from differential data1 version - Latest release: 21 days ago - 143 downloads total - 1 stars on GitHub - 1 maintainer
rmspc 1.8.0
Multiple Sample Peak Calling2 versions - Latest release: 6 months ago - 2.17 thousand downloads total - 18 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App2 versions - Latest release: 7 months ago - 4.01 thousand downloads total - 13 stars on GitHub - 1 maintainer
geneXtendeR 1.28.0
Optimized Functional Annotation Of ChIP-seq Data2 versions - Latest release: 6 months ago - 13.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
FindIT2 1.8.0
find influential TF and Target based on multi-omics data2 versions - Latest release: 6 months ago - 2.46 thousand downloads total - 6 stars on GitHub - 1 maintainer
sevenC 1.22.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs2 versions - Latest release: 6 months ago - 7.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
motifbreakR 2.16.0
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription F...2 versions - Latest release: 6 months ago - 19.6 thousand downloads total - 24 stars on GitHub - 1 maintainer
chromstaR 1.28.0
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data2 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
metagene2 1.18.0
A package to produce metagene plots2 versions - Latest release: 6 months ago - 6.63 thousand downloads total - 4 stars on GitHub - 1 maintainer
metagene 2.34.0
A package to produce metagene plots2 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets8 versions - Latest release: about 1 month ago - 2.02 thousand downloads total - 12 stars on GitHub - 1 maintainer
iSeq 1.54.0
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models2 versions - Latest release: 6 months ago - 23.6 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
nucleR 2.34.0
Nucleosome positioning package for R2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
STAN 2.28.0 removed
The Genomic STate ANnotation Package1 version - Latest release: 7 months ago - 14.8 thousand downloads total - 1 maintainer
ChIC 1.19.0 removed
Quality Control Pipeline for ChIP-Seq Data1 version - Latest release: 7 months ago - 6.47 thousand downloads total - 1 maintainer
Related Keywords
Software
97
Sequencing
64
Coverage
33
RNASeq
33
ImmunoOncology
24
Genetics
23
Transcription
23
Visualization
21
GeneExpression
21
QualityControl
18
ATACSeq
18
MultipleComparison
18
DataImport
18
FunctionalGenomics
16
Epigenetics
16
Normalization
13
DifferentialExpression
13
MethylSeq
12
GeneRegulation
12
Clustering
11
Alignment
11
DifferentialPeakCalling
11
Preprocessing
10
GenomeAnnotation
10
PeakDetection
9
GeneSetEnrichment
9
Annotation
9
Bayesian
8
ChipOnChip
8
bioconductor
8
Regression
8
Microarray
8
DNaseSeq
7
DNAMethylation
7
SystemsBiology
7
SequenceMatching
6
Transcriptomics
6
SingleCell
6
MotifAnnotation
6
r
6
AlternativeSplicing
5
BiomedicalInformatics
5
WorkflowStep
5
ReportWriting
5
BatchEffect
5
BiologicalQuestion
5
HistoneModification
5
Classification
5
CopyNumberVariation
5
ChIPchip
5
DNASeq
5
DifferentialMethylation
4
HiddenMarkovModel
4
chip-seq
4
HiC
4
CellBiology
4
PrincipalComponent
3
bioinformatics
3
Infrastructure
3
r-package
3
SNP
3
TimeCourse
3
GenomicVariation
2
StatisticalMethod
2
DNA3DStructure
2
GenomeWideAssociation
2
CpGIsland
2
GeneTarget
2
GraphAndNetwork
2
MethylationArray
2
Pathways
2
epigenetics
2
NucleosomePositioning
2
RiboSeq
2
Network
2
RIPSeq
2
rstats
2
DifferentialSplicing
2
bioconductor-package
2
ngs-analysis
1
overlapping-peaks
1
Scale simulation
1
next-generation-sequencing
1
mspc
1
genome-analysis
1
DataRepresentation
1
enriched-regions
1
analysis
1
rnaseq
1
derfinder
1
annotation-agnostic
1
WorkflowManagement
1
MotifDiscovery
1
interactive-reporting
1
html
1
genetics
1
comparison
1
benchmarking
1
benchmark
1
transcription-factors
1