bioconductor.org "ATACSeq" keyword
View the packages on the bioconductor.org package registry that are tagged with the "ATACSeq" keyword.
Top 2.4% on bioconductor.org
6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data6 versions - Latest release: about 1 month ago - 2 dependent packages - 299 thousand downloads total - 1 maintainer
cicero 1.28.0
Predict cis-co-accessibility from single-cell chromatin accessibility data6 versions - Latest release: about 1 month ago - 38 thousand downloads total - 1 maintainer
BiFET 1.30.0
Bias-free Footprint Enrichment Test6 versions - Latest release: about 1 month ago - 16.6 thousand downloads total - 1 maintainer
FindIT2 1.16.0
find influential TF and Target based on multi-omics data6 versions - Latest release: about 1 month ago - 8.27 thousand downloads total - 6 stars on GitHub - 1 maintainer
gVenn 1.0.0
Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions1 version - Latest release: 2 months ago - 600 downloads total - 0 stars on GitHub - 1 maintainer
poem 1.2.0
POpulation-based Evaluation Metrics3 versions - Latest release: about 2 months ago - 2.22 thousand downloads total - 8 stars on GitHub - 1 maintainer
miaSim 1.16.0
Microbiome Data Simulation6 versions - Latest release: about 1 month ago - 8.99 thousand downloads total - 22 stars on GitHub - 1 maintainer
COCOA 2.24.0
Coordinate Covariation Analysis6 versions - Latest release: about 1 month ago - 14.2 thousand downloads total - 1 maintainer
CelliD 1.18.0
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis7 versions - Latest release: about 1 month ago - 21.1 thousand downloads total - 1 maintainer
spatialHeatmap 2.15.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions15 versions - Latest release: about 1 month ago - 13.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
esATAC 1.32.0
An Easy-to-use Systematic pipeline for ATACseq data analysis6 versions - Latest release: about 1 month ago - 26.5 thousand downloads total - 23 stars on GitHub - 1 maintainer
CAEN 1.18.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq6 versions - Latest release: about 1 month ago - 7.67 thousand downloads total - 1 maintainer
ATACseqTFEA 1.12.0
Transcription Factor Enrichment Analysis for ATAC-seq6 versions - Latest release: about 2 months ago - 7.02 thousand downloads total - 1 stars on GitHub - 1 maintainer
fCCAC 1.36.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...6 versions - Latest release: about 1 month ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
RepViz 1.25.0
Replicate oriented Visualization of a genomic region6 versions - Latest release: about 1 month ago - 11.2 thousand downloads total - 1 maintainer
MACSr 1.18.0
MACS: Model-based Analysis for ChIP-Seq6 versions - Latest release: about 1 month ago - 11.6 thousand downloads total - 1 maintainer
epigraHMM 1.18.0
Epigenomic R-based analysis with hidden Markov models7 versions - Latest release: about 1 month ago - 12.3 thousand downloads total - 1 maintainer
nullranges 1.16.3
Generation of null ranges via bootstrapping or covariate matching7 versions - Latest release: 10 days ago - 1 dependent package - 14.8 thousand downloads total - 22 stars on GitHub - 1 maintainer
metaseqR2 1.22.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...6 versions - Latest release: about 1 month ago - 11.5 thousand downloads total - 1 maintainer
GRaNIE 1.14.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...6 versions - Latest release: about 1 month ago - 9.43 thousand downloads total - 1 maintainer
ATACseqQC 1.34.0
ATAC-seq Quality Control6 versions - Latest release: about 1 month ago - 2 dependent packages - 64.3 thousand downloads total - 1 maintainer
bcSeq 1.32.0
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens6 versions - Latest release: about 1 month ago - 14.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
ChromSCape 1.20.0
Analysis of single-cell epigenomics datasets with a Shiny App6 versions - Latest release: about 2 months ago - 9.56 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
6 versions - Latest release: about 1 month ago - 4 dependent packages - 123 thousand downloads total - 370 stars on GitHub - 1 maintainer
PCAtools 2.21.0
PCAtools: Everything Principal Components Analysis6 versions - Latest release: about 1 month ago - 4 dependent packages - 123 thousand downloads total - 370 stars on GitHub - 1 maintainer
scBFA 1.24.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...6 versions - Latest release: about 2 months ago - 11.2 thousand downloads total - 1 maintainer
simPIC 1.6.0
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data4 versions - Latest release: about 2 months ago - 4.43 thousand downloads total - 0 stars on GitHub - 1 maintainer
DegCre 1.6.0
Probabilistic association of DEGs to CREs from differential data4 versions - Latest release: about 2 months ago - 5.01 thousand downloads total - 5 stars on GitHub - 1 maintainer
airpart 1.18.0
Differential cell-type-specific allelic imbalance6 versions - Latest release: about 2 months ago - 10.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
GeoTcgaData 2.10.0
Processing Various Types of Data on GEO and TCGA6 versions - Latest release: about 2 months ago - 7.97 thousand downloads total - 28 stars on GitHub - 1 maintainer
recoup 1.38.0
An R package for the creation of complex genomic profile plots6 versions - Latest release: about 2 months ago - 17.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
VplotR 1.20.0
Set of tools to make V-plots and compute footprint profiles7 versions - Latest release: about 2 months ago - 9.64 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
7 versions - Latest release: about 2 months ago - 1 dependent package - 153 thousand downloads total - 210 stars on GitHub - 1 maintainer
scDblFinder 1.24.0
scDblFinder7 versions - Latest release: about 2 months ago - 1 dependent package - 153 thousand downloads total - 210 stars on GitHub - 1 maintainer
EpiCompare 1.14.0
Comparison, Benchmarking & QC of Epigenomic Datasets15 versions - Latest release: about 1 month ago - 6.37 thousand downloads total - 17 stars on GitHub - 1 maintainer
mnem 1.26.0
Mixture Nested Effects Models6 versions - Latest release: about 1 month ago - 4 dependent packages - 14.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
nempi 1.18.0
Inferring unobserved perturbations from gene expression data6 versions - Latest release: about 1 month ago - 7.82 thousand downloads total - 2 stars on GitHub - 1 maintainer
chromstaR 1.34.0 removed
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data5 versions - Latest release: 8 months ago - 19.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
compartmap 1.20.0 removed
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq3 versions - Latest release: about 2 years ago - 6.72 thousand downloads total - 11 stars on GitHub - 1 maintainer
HicAggR 1.2.0
Set of 3D genomic interaction analysis tools3 versions - Latest release: about 1 year ago - 1.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
BRGenomics 1.18.0 removed
Tools for the Efficient Analysis of High-Resolution Genomics Data6 versions - Latest release: about 1 year ago - 1 dependent package - 8.91 thousand downloads total - 1 maintainer
Related Keywords
Software
39
Sequencing
20
ChIPSeq
19
RNASeq
18
GeneExpression
14
SingleCell
14
Epigenetics
12
GeneRegulation
12
ImmunoOncology
11
DNaseSeq
9
Coverage
8
QualityControl
8
Clustering
7
FunctionalGenomics
7
Visualization
7
DNASeq
7
Transcription
7
MultipleComparison
6
Normalization
5
DataImport
5
Preprocessing
5
DifferentialExpression
5
GeneSetEnrichment
5
CellBiology
4
GraphAndNetwork
4
SystemsBiology
4
Genetics
4
GeneTarget
4
Alignment
4
Network
4
bioconductor
4
NetworkInference
3
PrincipalComponent
3
Transcriptomics
3
Regression
3
BatchEffect
3
Classification
3
HiddenMarkovModel
3
CRISPR
3
Pathways
3
BiomedicalInformatics
3
DifferentialMethylation
3
DimensionReduction
3
DataRepresentation
3
Annotation
3
DifferentialPeakCalling
3
ReportWriting
3
RIPSeq
3
HistoneModification
3
MethylSeq
3
WorkflowStep
2
PooledScreens
2
r-package
2
scatac-seq
2
single-cell
2
NucleosomePositioning
2
GenomicVariation
2
MNaseSeq
2
Spatial
2
MethylationArray
2
Microarray
2
GenomeAnnotation
2
PeakDetection
2
CellBasedAssays
2
DNAMethylation
2
benchmarking
1
benchmark
1
doublets
1
BiologicalQuestion
1
ChipOnChip
1
SNP
1
CopyNumberVariation
1
TranscriptomeVariant
1
bioc-devel
1
bioconductor-package
1
comparison
1
epigenetics
1
genetics
1
html
1
interactive-reporting
1
GeneSignaling
1
NeuralNetwork
1
scrna-seq
1
DNA3DStructure
1
HiC
1
r
1
GenomeWideAssociation
1
bootstrap
1
genomics
1
matching
1
statistics
1
AlternativeSplicing
1
pipeline
1
Bayesian
1
atac-seq
1
DifferentialSplicing
1
ProprietaryPlatforms
1
TissueMicroarray
1
TimeCourse
1
MultipleSequenceAlignment
1