bioconductor.org "ATACSeq" keyword
View the packages on the bioconductor.org package registry that are tagged with the "ATACSeq" keyword.
VplotR 1.18.0
Set of tools to make V-plots and compute footprint profiles6 versions - Latest release: 3 months ago - 8.23 thousand downloads total - 11 stars on GitHub - 1 maintainer
EpiCompare 1.12.0
Comparison, Benchmarking & QC of Epigenomic Datasets13 versions - Latest release: 3 months ago - 5.03 thousand downloads total - 17 stars on GitHub - 1 maintainer
fCCAC 1.34.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...5 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
esATAC 1.30.0
An Easy-to-use Systematic pipeline for ATACseq data analysis5 versions - Latest release: 3 months ago - 25 thousand downloads total - 23 stars on GitHub - 1 maintainer
recoup 1.36.0
An R package for the creation of complex genomic profile plots5 versions - Latest release: 3 months ago - 15.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
BiFET 1.28.0
Bias-free Footprint Enrichment Test5 versions - Latest release: 3 months ago - 15 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 103 thousand downloads total - 199 stars on GitHub - 1 maintainer
scDblFinder 1.22.0
scDblFinder6 versions - Latest release: 3 months ago - 1 dependent package - 103 thousand downloads total - 199 stars on GitHub - 1 maintainer
scBFA 1.22.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...5 versions - Latest release: 3 months ago - 9.72 thousand downloads total - 1 maintainer
GRaNIE 1.12.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...5 versions - Latest release: 3 months ago - 8.02 thousand downloads total - 1 maintainer
metaseqR2 1.20.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...5 versions - Latest release: 3 months ago - 9.84 thousand downloads total - 1 maintainer
CAEN 1.16.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq5 versions - Latest release: 3 months ago - 6.49 thousand downloads total - 1 maintainer
epigraHMM 1.16.0
Epigenomic R-based analysis with hidden Markov models5 versions - Latest release: 3 months ago - 7.21 thousand downloads total - 1 maintainer
airpart 1.16.0
Differential cell-type-specific allelic imbalance5 versions - Latest release: 3 months ago - 9.42 thousand downloads total - 2 stars on GitHub - 1 maintainer
bcSeq 1.30.0
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens5 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MACSr 1.16.0
MACS: Model-based Analysis for ChIP-Seq5 versions - Latest release: 3 months ago - 10.1 thousand downloads total - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions14 versions - Latest release: about 1 month ago - 12.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
simPIC 1.4.0
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data3 versions - Latest release: 3 months ago - 3.38 thousand downloads total - 0 stars on GitHub - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis5 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA5 versions - Latest release: 3 months ago - 6.59 thousand downloads total - 26 stars on GitHub - 1 maintainer
DegCre 1.4.0
Probabilistic association of DEGs to CREs from differential data3 versions - Latest release: 3 months ago - 3.49 thousand downloads total - 5 stars on GitHub - 1 maintainer
RepViz 1.24.0
Replicate oriented Visualization of a genomic region5 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 269 thousand downloads total - 1 maintainer
DiffBind 3.18.0
Differential Binding Analysis of ChIP-Seq Peak Data5 versions - Latest release: 3 months ago - 2 dependent packages - 269 thousand downloads total - 1 maintainer
chromstaR 1.34.0
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data5 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 8 stars on GitHub - 1 maintainer
miaSim 1.14.0
Microbiome Data Simulation5 versions - Latest release: 3 months ago - 7.47 thousand downloads total - 22 stars on GitHub - 1 maintainer
FindIT2 1.14.0
find influential TF and Target based on multi-omics data5 versions - Latest release: 2 months ago - 6.68 thousand downloads total - 6 stars on GitHub - 1 maintainer
nullranges 1.14.0
Generation of null ranges via bootstrapping or covariate matching5 versions - Latest release: 3 months ago - 1 dependent package - 11 thousand downloads total - 22 stars on GitHub - 1 maintainer
poem 1.0.1
POpulation-based Evaluation Metrics2 versions - Latest release: 2 months ago - 1.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models5 versions - Latest release: 3 months ago - 4 dependent packages - 13.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
ATACseqQC 1.32.0
ATAC-seq Quality Control5 versions - Latest release: 3 months ago - 2 dependent packages - 56.8 thousand downloads total - 1 maintainer
CelliD 1.16.0
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis6 versions - Latest release: 2 months ago - 18.1 thousand downloads total - 1 maintainer
ChromSCape 1.17.0
Analysis of single-cell epigenomics datasets with a Shiny App5 versions - Latest release: 3 months ago - 7.92 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 96.4 thousand downloads total - 352 stars on GitHub - 1 maintainer
PCAtools 2.20.0
PCAtools: Everything Principal Components Analysis5 versions - Latest release: 3 months ago - 4 dependent packages - 96.4 thousand downloads total - 352 stars on GitHub - 1 maintainer
cicero 1.26.0
Predict cis-co-accessibility from single-cell chromatin accessibility data5 versions - Latest release: 3 months ago - 30.2 thousand downloads total - 1 maintainer
ATACseqTFEA 1.10.0
Transcription Factor Enrichment Analysis for ATAC-seq5 versions - Latest release: 3 months ago - 5.51 thousand downloads total - 1 stars on GitHub - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 3 months ago - 6.41 thousand downloads total - 2 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: over 1 year ago - 6.72 thousand downloads total - 11 stars on GitHub - 1 maintainer
BRGenomics 1.18.0 removed
Tools for the Efficient Analysis of High-Resolution Genomics Data6 versions - Latest release: 8 months ago - 1 dependent package - 8.91 thousand downloads total - 1 maintainer
HicAggR 1.2.0
Set of 3D genomic interaction analysis tools3 versions - Latest release: 8 months ago - 1.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
38
Sequencing
19
RNASeq
18
ChIPSeq
18
GeneExpression
14
SingleCell
14
GeneRegulation
12
Epigenetics
11
ImmunoOncology
11
DNaseSeq
9
QualityControl
8
Coverage
8
Clustering
7
FunctionalGenomics
7
DNASeq
7
Transcription
7
MultipleComparison
6
Visualization
6
DifferentialExpression
5
Normalization
5
Preprocessing
5
GeneSetEnrichment
5
DataImport
5
SystemsBiology
4
CellBiology
4
GraphAndNetwork
4
GeneTarget
4
bioconductor
4
Network
4
Genetics
4
Alignment
4
Annotation
3
Regression
3
NetworkInference
3
BiomedicalInformatics
3
ReportWriting
3
HistoneModification
3
Classification
3
HiddenMarkovModel
3
DifferentialPeakCalling
3
CRISPR
3
DifferentialMethylation
3
PrincipalComponent
3
MethylSeq
3
Transcriptomics
3
DimensionReduction
3
BatchEffect
3
RIPSeq
3
Pathways
3
DataRepresentation
2
CellBasedAssays
2
Microarray
2
Spatial
2
NucleosomePositioning
2
WorkflowStep
2
r-package
2
MNaseSeq
2
PooledScreens
2
PeakDetection
2
scatac-seq
2
MethylationArray
2
DNAMethylation
2
GenomeAnnotation
2
GenomicVariation
2
single-cell
2
HiC
1
CopyNumberVariation
1
DNA3DStructure
1
r
1
scrna-seq
1
NeuralNetwork
1
SNP
1
GeneSignaling
1
shiny
1
epigenomics
1
ShinyApps
1
Microbiome
1
statistics
1
matching
1
genomics
1
GenomeWideAssociation
1
bootstrap
1
BiologicalQuestion
1
benchmark
1
benchmarking
1
bioconductor-package
1
comparison
1
epigenetics
1
genetics
1
html
1
interactive-reporting
1
bioc-devel
1
atac-seq
1
pipeline
1
ChipOnChip
1
doublets
1
KEGG
1
AlternativeSplicing
1
Bayesian
1
DifferentialSplicing
1