Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "ATACSeq" keyword
simPIC 1.0.0
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data1 version - Latest release: about 1 month ago - 345 downloads total - 0 stars on GitHub - 1 maintainer
DegCre 1.0.0
Probabilistic association of DEGs to CREs from differential data1 version - Latest release: about 1 month ago - 361 downloads total - 1 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
miaSim 1.8.0
Microbiome Data Simulation3 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 15 stars on GitHub - 1 maintainer
FindIT2 1.8.0
find influential TF and Target based on multi-omics data3 versions - Latest release: 7 months ago - 2.77 thousand downloads total - 6 stars on GitHub - 1 maintainer
chromstaR 1.28.0
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data3 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 7 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
compartmap 1.20.0
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq3 versions - Latest release: 6 months ago - 6.35 thousand downloads total - 11 stars on GitHub - 1 maintainer
CelliD 1.10.1
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis4 versions - Latest release: 6 months ago - 9.32 thousand downloads total - 1 maintainer
MACSr 1.10.0
MACS: Model-based Analysis for ChIP-Seq3 versions - Latest release: 7 months ago - 5.49 thousand downloads total - 1 maintainer
epigraHMM 1.10.0
Epigenomic R-based analysis with hidden Markov models3 versions - Latest release: 7 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: 7 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: 7 months ago - 8.91 thousand downloads total - 1 maintainer
CAEN 1.10.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq3 versions - Latest release: 7 months ago - 2.78 thousand downloads total - 1 maintainer
RepViz 1.18.0
Replicate oriented Visualization of a genomic region3 versions - Latest release: 7 months ago - 6.28 thousand downloads total - 1 maintainer
esATAC 1.24.0
An Easy-to-use Systematic pipeline for ATACseq data analysis3 versions - Latest release: 7 months ago - 20.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
scBFA 1.16.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...3 versions - Latest release: 7 months ago - 5.39 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: 7 months ago - 3.75 thousand downloads total - 1 maintainer
BRGenomics 1.14.1
Tools for the Efficient Analysis of High-Resolution Genomics Data4 versions - Latest release: 3 months ago - 1 dependent package - 8.07 thousand downloads total - 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: 7 months ago - 5.12 thousand downloads total - 1 maintainer
GeoTcgaData 2.2.0
Processing Various Types of Data on GEO and TCGA3 versions - Latest release: 7 months ago - 1.61 thousand downloads total - 21 stars on GitHub - 1 maintainer
fCCAC 1.28.0
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing ...3 versions - Latest release: 7 months ago - 9.84 thousand downloads total - 1 maintainer
ATACseqQC 1.26.0
ATAC-seq Quality Control3 versions - Latest release: 7 months ago - 2 dependent packages - 42.4 thousand downloads total - 1 maintainer
bcSeq 1.24.0
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens3 versions - Latest release: 7 months ago - 8.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
COCOA 2.16.0
Coordinate Covariation Analysis3 versions - Latest release: 7 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: 7 months ago - 21.1 thousand downloads total - 1 maintainer
airpart 1.10.0
Differential cell-type-specific allelic imbalance3 versions - Latest release: 7 months ago - 3.63 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 57.3 thousand downloads total - 130 stars on GitHub - 1 maintainer
scDblFinder 1.16.0
scDblFinder3 versions - Latest release: 7 months ago - 1 dependent package - 57.3 thousand downloads total - 130 stars on GitHub - 1 maintainer
recoup 1.32.0
An R package for the creation of complex genomic profile plots3 versions - Latest release: 20 days ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
spatialHeatmap 2.10.0
spatialHeatmap8 versions - Latest release: 19 days ago - 5.78 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 28 days ago - 4 dependent packages - 67.6 thousand downloads total - 315 stars on GitHub - 1 maintainer
PCAtools 2.16.0
PCAtools: Everything Principal Components Analysis3 versions - Latest release: 28 days ago - 4 dependent packages - 67.6 thousand downloads total - 315 stars on GitHub - 1 maintainer
HicAggR 1.0.0
Set of 3D genomic interaction analysis tools1 version - Latest release: about 1 month ago - 82 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 25 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: 25 days ago - 2 dependent packages - 227 thousand downloads total - 1 maintainer
ATACseqTFEA 1.6.0
Transcription Factor Enrichment Analysis for ATAC-seq3 versions - Latest release: 28 days ago - 1.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
nempi 1.12.0
Inferring unobserved perturbations from gene expression data3 versions - Latest release: about 1 month ago - 2.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
mnem 1.20.0
Mixture Nested Effects Models3 versions - Latest release: about 1 month ago - 4 dependent packages - 8.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
VplotR 1.14.0
Set of tools to make V-plots and compute footprint profiles4 versions - Latest release: about 1 month ago - 3.73 thousand downloads total - 8 stars on GitHub - 1 maintainer
Related Keywords
Software
37
Sequencing
19
ChIPSeq
18
RNASeq
17
GeneExpression
14
SingleCell
13
GeneRegulation
12
ImmunoOncology
11
Epigenetics
11
DNaseSeq
9
Coverage
8
QualityControl
8
FunctionalGenomics
7
DNASeq
7
Transcription
7
MultipleComparison
6
Clustering
6
DataImport
5
DifferentialExpression
5
Visualization
5
Preprocessing
5
Normalization
5
GeneSetEnrichment
5
Alignment
4
CellBiology
4
SystemsBiology
4
Network
4
GeneTarget
4
Genetics
4
BiomedicalInformatics
3
GraphAndNetwork
3
NetworkInference
3
Regression
3
DifferentialMethylation
3
Transcriptomics
3
RIPSeq
3
bioconductor
3
Annotation
3
HistoneModification
3
HiddenMarkovModel
3
BatchEffect
3
Classification
3
CRISPR
3
DifferentialPeakCalling
3
MethylSeq
3
Pathways
3
ReportWriting
3
PrincipalComponent
3
GenomicVariation
2
WorkflowStep
2
PooledScreens
2
DataRepresentation
2
CellBasedAssays
2
DNAMethylation
2
NucleosomePositioning
2
MethylationArray
2
Microarray
2
MNaseSeq
2
PeakDetection
2
GenomeAnnotation
2
DimensionReduction
2
single-cell
2
r-package
2
benchmarking
1
benchmark
1
SNP
1
Microbiome
1
MultipleSequenceAlignment
1
SequenceMatching
1
shiny
1
TranscriptomeVariant
1
doublets
1
ChipOnChip
1
epigenomics
1
Spatial
1
TissueMicroarray
1
DNA3DStructure
1
HiC
1
r
1
GeneSignaling
1
NeuralNetwork
1
ShinyApps
1
BiologicalQuestion
1
statistics
1
matching
1
genomics
1
bootstrap
1
GenomeWideAssociation
1
atac-seq
1
pipeline
1
KEGG
1
scrna-seq
1
scatac-seq
1
interactive-reporting
1
html
1
AlternativeSplicing
1
Bayesian
1
genetics
1
DifferentialSplicing
1
ProprietaryPlatforms
1