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: 5 months ago - 8.58 thousand downloads total - 11 stars on GitHub - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 4 months ago - 7.12 thousand downloads total - 2 stars on GitHub - 1 maintainer
fCCAC 1.34.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...5 versions - Latest release: 4 months ago - 14.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions14 versions - Latest release: 2 months ago - 12.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA5 versions - Latest release: 4 months ago - 6.88 thousand downloads total - 28 stars on GitHub - 1 maintainer
esATAC 1.30.0
An Easy-to-use Systematic pipeline for ATACseq data analysis5 versions - Latest release: 4 months ago - 25.3 thousand downloads total - 23 stars on GitHub - 1 maintainer
GRaNIE 1.12.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...5 versions - Latest release: 4 months ago - 8.31 thousand downloads total - 1 maintainer
EpiCompare 1.12.0
Comparison, Benchmarking & QC of Epigenomic Datasets13 versions - Latest release: 4 months ago - 5.27 thousand downloads total - 17 stars on GitHub - 1 maintainer
RepViz 1.24.0
Replicate oriented Visualization of a genomic region5 versions - Latest release: 4 months ago - 10.5 thousand downloads total - 1 maintainer
MACSr 1.16.0
MACS: Model-based Analysis for ChIP-Seq5 versions - Latest release: 4 months ago - 10.4 thousand downloads total - 1 maintainer
miaSim 1.14.0
Microbiome Data Simulation5 versions - Latest release: 4 months ago - 7.74 thousand downloads total - 22 stars on GitHub - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models5 versions - Latest release: 5 months ago - 4 dependent packages - 13.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 4 months ago - 2 dependent packages - 271 thousand downloads total - 1 maintainer
DiffBind 3.18.0
Differential Binding Analysis of ChIP-Seq Peak Data5 versions - Latest release: 4 months ago - 2 dependent packages - 271 thousand downloads total - 1 maintainer
chromstaR 1.34.0
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data5 versions - Latest release: 4 months ago - 19.4 thousand downloads total - 8 stars on GitHub - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis5 versions - Latest release: 4 months ago - 12 thousand downloads total - 1 maintainer
BiFET 1.28.0
Bias-free Footprint Enrichment Test5 versions - Latest release: 4 months ago - 15.3 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: 5 months ago - 6.75 thousand downloads total - 1 maintainer
epigraHMM 1.16.0
Epigenomic R-based analysis with hidden Markov models5 versions - Latest release: 4 months ago - 7.59 thousand downloads total - 1 maintainer
DegCre 1.4.0
Probabilistic association of DEGs to CREs from differential data3 versions - Latest release: 4 months ago - 4.21 thousand downloads total - 5 stars on GitHub - 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: 4 months ago - 10.1 thousand downloads total - 1 maintainer
recoup 1.36.0
An R package for the creation of complex genomic profile plots5 versions - Latest release: 4 months ago - 15.9 thousand downloads total - 1 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: 4 months ago - 9.99 thousand downloads total - 1 maintainer
airpart 1.16.0
Differential cell-type-specific allelic imbalance5 versions - Latest release: 4 months ago - 9.7 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: 4 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
FindIT2 1.14.0
find influential TF and Target based on multi-omics data5 versions - Latest release: 4 months ago - 7 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: 4 months ago - 1 dependent package - 11.5 thousand downloads total - 22 stars on GitHub - 1 maintainer
ATACseqQC 1.32.0
ATAC-seq Quality Control5 versions - Latest release: 4 months ago - 2 dependent packages - 58.2 thousand downloads total - 1 maintainer
cicero 1.26.0
Predict cis-co-accessibility from single-cell chromatin accessibility data5 versions - Latest release: 4 months ago - 31 thousand downloads total - 1 maintainer
poem 1.0.1
POpulation-based Evaluation Metrics2 versions - Latest release: 4 months ago - 1.33 thousand downloads total - 7 stars on GitHub - 1 maintainer
CelliD 1.16.0
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis6 versions - Latest release: 4 months ago - 18.6 thousand downloads total - 1 maintainer
ChromSCape 1.17.0
Analysis of single-cell epigenomics datasets with a Shiny App5 versions - Latest release: 4 months ago - 8.15 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
5 versions - Latest release: 4 months ago - 4 dependent packages - 98.1 thousand downloads total - 355 stars on GitHub - 1 maintainer
PCAtools 2.20.0
PCAtools: Everything Principal Components Analysis5 versions - Latest release: 4 months ago - 4 dependent packages - 98.1 thousand downloads total - 355 stars on GitHub - 1 maintainer
ATACseqTFEA 1.10.0
Transcription Factor Enrichment Analysis for ATAC-seq5 versions - Latest release: 4 months ago - 5.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 105 thousand downloads total - 204 stars on GitHub - 1 maintainer
scDblFinder 1.22.0
scDblFinder6 versions - Latest release: 4 months ago - 1 dependent package - 105 thousand downloads total - 204 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: 5 months ago - 3.38 thousand downloads total - 0 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: almost 2 years 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: 10 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: 9 months ago - 1.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software
38
Sequencing
19
RNASeq
18
ChIPSeq
18
SingleCell
14
GeneExpression
14
GeneRegulation
12
ImmunoOncology
11
Epigenetics
11
DNaseSeq
9
Coverage
8
QualityControl
8
DNASeq
7
FunctionalGenomics
7
Transcription
7
Clustering
7
MultipleComparison
6
Visualization
6
Preprocessing
5
DifferentialExpression
5
GeneSetEnrichment
5
Normalization
5
DataImport
5
bioconductor
4
GraphAndNetwork
4
Genetics
4
GeneTarget
4
CellBiology
4
SystemsBiology
4
Alignment
4
Network
4
Classification
3
DifferentialMethylation
3
BiomedicalInformatics
3
CRISPR
3
DifferentialPeakCalling
3
HistoneModification
3
NetworkInference
3
MethylSeq
3
Pathways
3
Regression
3
RIPSeq
3
ReportWriting
3
HiddenMarkovModel
3
Transcriptomics
3
PrincipalComponent
3
BatchEffect
3
DimensionReduction
3
Annotation
3
GenomicVariation
2
r-package
2
WorkflowStep
2
PeakDetection
2
GenomeAnnotation
2
single-cell
2
scatac-seq
2
MNaseSeq
2
Microarray
2
CellBasedAssays
2
Spatial
2
NucleosomePositioning
2
DataRepresentation
2
PooledScreens
2
DNAMethylation
2
MethylationArray
2
KEGG
1
TranscriptomeVariant
1
MultipleSequenceAlignment
1
SequenceMatching
1
GenomeWideAssociation
1
bootstrap
1
genomics
1
matching
1
statistics
1
ShinyApps
1
epigenomics
1
shiny
1
bioc-devel
1
doublets
1
bioinformatics
1
simulation
1
scrna-seq
1
DNA3DStructure
1
HiC
1
r
1
benchmarking
1
bioconductor-package
1
comparison
1
epigenetics
1
genetics
1
html
1
interactive-reporting
1
benchmark
1
pipeline
1
Microbiome
1
GeneSignaling
1
atac-seq
1
NeuralNetwork
1
BiologicalQuestion
1
SNP
1